Human INPP5DA - XChem results

Click event map in table to view a different crystal / compound pair

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Ligand-bound models for Summary

Interpreting 'Ligand confidence'

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.

Interpreting 'Model status':

6 - Deposited: The model has been deposited in the PDB.
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.

Interpreting 'Ligand validation' spider plots:

Each axis represents one of the values described below; small is better, and large values on any axis implies that further investigation is warranted.

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)

Crystal ID PDB ID Ligand ID Ligand confidence Model status Compound Ligand Validation Event Map 3D Resol SPG/ Cell Files
INPP5DA-x0019 None LIG-A-901 not assigned 4 - CompChem ready
1.22 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0020 None LIG-A-901 not assigned 4 - CompChem ready
1.37 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0021 None LIG-A-901 not assigned 4 - CompChem ready
1.31 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0027 None LIG-A-901 not assigned 4 - CompChem ready
1.38 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0030 None LIG-A-901 not assigned 4 - CompChem ready
1.32 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0039 None LIG-A-901 not assigned 4 - CompChem ready
1.23 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0040 None LIG-A-901 not assigned 4 - CompChem ready
1.27 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0054 None LIG-A-901 not assigned 4 - CompChem ready
1.45 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0058 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0058 None LIG-A-1101 4 - High Confidence 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0058 None LIG-A-901 not assigned 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0062 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.25 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0062 None LIG-A-901 not assigned 4 - CompChem ready
1.25 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0067 None LIG-A-901 not assigned 4 - CompChem ready
1.40 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0073 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0073 None LIG-A-901 not assigned 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0075 None LIG-A-901 not assigned 4 - CompChem ready
1.34 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0083 None LIG-A-901 not assigned 4 - CompChem ready
1.35 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0084 None LIG-A-901 not assigned 4 - CompChem ready
1.46 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0088 None LIG-A-901 not assigned 4 - CompChem ready
1.56 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0092 None LIG-A-901 not assigned 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0097 None LIG-A-901 not assigned 4 - CompChem ready
1.26 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0100 None LIG-A-901 not assigned 4 - CompChem ready
1.32 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0101 None LIG-A-901 not assigned 4 - CompChem ready
1.37 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0103 None LIG-A-1001 2 - Correct ligand, weak density 4 - CompChem ready
1.36 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0103 None LIG-A-901 not assigned 4 - CompChem ready
1.36 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0106 None LIG-A-901 not assigned 4 - CompChem ready
1.38 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0114 None LIG-A-901 not assigned 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0118 None LIG-A-901 not assigned 4 - CompChem ready
1.48 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0119 None LIG-A-901 not assigned 4 - CompChem ready
1.32 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0121 None LIG-A-901 not assigned 4 - CompChem ready
1.43 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0126 None LIG-A-901 not assigned 4 - CompChem ready
1.28 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0129 None LIG-A-901 not assigned 4 - CompChem ready
1.43 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0133 None LIG-A-901 not assigned 4 - CompChem ready
1.37 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0140 None LIG-A-901 not assigned 4 - CompChem ready
1.25 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0141 None LIG-A-901 not assigned 4 - CompChem ready
1.16 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0148 None LIG-A-901 not assigned 4 - CompChem ready
1.34 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0152 None LIG-A-901 not assigned 4 - CompChem ready
1.35 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0154 None LIG-A-901 not assigned 4 - CompChem ready
1.42 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0161 None LIG-A-901 not assigned 4 - CompChem ready
1.43 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0163 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.31 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0163 None LIG-A-901 not assigned 4 - CompChem ready
1.31 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0169 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.27 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0169 None LIG-A-901 not assigned 4 - CompChem ready
1.27 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0174 None LIG-A-901 not assigned 4 - CompChem ready
1.45 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0176 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.35 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0176 None LIG-A-901 not assigned 4 - CompChem ready
1.35 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0182 None LIG-A-901 not assigned 4 - CompChem ready
1.28 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0183 None LIG-A-901 not assigned 4 - CompChem ready
1.45 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0194 None LIG-A-901 not assigned 4 - CompChem ready
1.36 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0195 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.34 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0195 None LIG-A-901 not assigned 4 - CompChem ready
1.34 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0200 None LIG-A-901 not assigned 4 - CompChem ready
1.29 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0201 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.24 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0201 None LIG-A-901 not assigned 4 - CompChem ready
1.24 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0221 None LIG-A-901 not assigned 4 - CompChem ready
1.58 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0239 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.59 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0239 None LIG-A-901 not assigned 4 - CompChem ready
1.59 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0243 None LIG-A-901 not assigned 4 - CompChem ready
1.33 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0251 None LIG-A-901 not assigned 4 - CompChem ready
1.25 P 21 21 21
62 78 88 90 90 90		 Save
INPP5DA-x0300 None LIG-A-901 not assigned 4 - CompChem ready
1.26 P 21 21 21
62 78 88 90 90 90		 Save
INPP5DA-x0302 None LIG-A-901 not assigned 4 - CompChem ready
1.52 P 21 21 21
62 78 88 90 90 90		 Save
INPP5DA-x0303 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.42 P 21 21 21
62 78 88 90 90 90		 Save
INPP5DA-x0303 None LIG-A-901 not assigned 4 - CompChem ready
1.42 P 21 21 21
62 78 88 90 90 90		 Save
INPP5DA-x0311 None LIG-A-901 not assigned 4 - CompChem ready
1.74 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0316 None LIG-A-901 not assigned 4 - CompChem ready
1.52 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0320 None LIG-A-901 not assigned 4 - CompChem ready
1.46 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0325 None LIG-A-901 not assigned 4 - CompChem ready
1.49 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0340 None LIG-A-901 not assigned 4 - CompChem ready
1.46 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0342 None LIG-A-901 not assigned 4 - CompChem ready
1.71 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0345 None LIG-A-901 not assigned 4 - CompChem ready
1.53 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0350 None LIG-A-901 not assigned 4 - CompChem ready
1.65 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0358 None LIG-A-901 not assigned 4 - CompChem ready
1.40 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0359 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.37 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0359 None LIG-A-901 not assigned 4 - CompChem ready
1.37 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0361 None LIG-A-901 not assigned 4 - CompChem ready
1.63 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0368 None LIG-A-901 not assigned 4 - CompChem ready
1.64 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0378 None LIG-A-901 not assigned 4 - CompChem ready
1.50 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0382 None LIG-A-901 not assigned 4 - CompChem ready
1.34 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0401 None LIG-A-901 not assigned 4 - CompChem ready
1.43 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0403 None LIG-A-901 not assigned 4 - CompChem ready
1.40 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0417 None LIG-A-901 not assigned 4 - CompChem ready
1.56 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0423 None LIG-A-901 not assigned 4 - CompChem ready
1.98 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0438 None LIG-A-901 not assigned 4 - CompChem ready
1.52 P 21 21 21
62 78 88 90 90 90		 Save
INPP5DA-x0449 None LIG-A-901 not assigned 4 - CompChem ready
1.54 P 21 21 21
62 78 89 90 90 90		 Save
INPP5DA-x0469 None LIG-A-901 not assigned 4 - CompChem ready
1.50 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0479 None LIG-A-901 not assigned 4 - CompChem ready
1.47 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0490 None LIG-A-1001 2 - Correct ligand, weak density 4 - CompChem ready
1.54 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0490 None LIG-A-901 not assigned 4 - CompChem ready
1.54 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0494 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.74 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0494 None LIG-A-901 not assigned 4 - CompChem ready
1.74 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0510 None LIG-A-901 not assigned 4 - CompChem ready
1.60 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0518 None LIG-A-901 not assigned 4 - CompChem ready
1.43 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0524 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.52 P 21 21 21
62 79 88 90 90 90		 Save
INPP5DA-x0524 None LIG-A-901 not assigned 4 - CompChem ready
1.52 P 21 21 21
62 79 88 90 90 90		 Save
INPP5DA-x0527 None LIG-A-1001 4 - High Confidence 4 - CompChem ready
1.32 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0527 None LIG-A-1101 2 - Correct ligand, weak density 4 - CompChem ready
1.32 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0527 None LIG-A-901 not assigned 4 - CompChem ready
1.32 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0542 None LIG-A-901 not assigned 4 - CompChem ready
1.55 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0543 None LIG-A-901 not assigned 4 - CompChem ready
1.56 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0558 None LIG-A-901 not assigned 4 - CompChem ready
1.60 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0560 None LIG-A-901 not assigned 4 - CompChem ready
1.70 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0573 None LIG-A-901 not assigned 4 - CompChem ready
1.49 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0577 None LIG-A-901 not assigned 4 - CompChem ready
1.47 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0588 None LIG-A-901 not assigned 4 - CompChem ready
1.72 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0590 None LIG-A-901 not assigned 4 - CompChem ready
1.45 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0596 None LIG-A-901 not assigned 4 - CompChem ready
1.42 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0604 None LIG-A-901 not assigned 4 - CompChem ready
1.55 P 21 21 21
62 79 89 90 90 90		 Save
INPP5DA-x0609 None LIG-A-901 not assigned 4 - CompChem ready
1.55 P 21 21 21
62 78 89 90 90 90		 Save