JMJD2D Fragment Hits

Ligand-bound models for JMJD2D

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.)

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Model Name	Compound SMILES	Compound Structure	Site Name	Ligand Confidence	Model Status	Ligand Validation	Event Map 3D	Comment	PDB Identifier	Resol	Spacegroup	Cell	PDB	MTZ	Event Map
Model Name	Compound SMILES	Compound Structure	Site Name	Ligand Confidence	Model Status	Ligand Validation	Event Map 3D	Comment	PDB Identifier	Resol	Spacegroup	Cell	PDB	Event Map	MTZ
JMJD2DA-x336_event2	c1cc2c(cc1N)nc(C(F)(F)F)[nH]2		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.34	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x365_event2	CC(c1c[nH]c2ccccc12)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.25	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x376_event1	Cc1ccc(cn1)C(N)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.45	P 41 21 2	71 71 149 90 90 90	Save	Save	Save
JMJD2DA-x378_event1	Cc1cc2c(cc1C)[nH]cn2		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.24	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x386_event1	Cc1ccc(C(N)=O)cn1		None	3 - Clear density, unexpected ligand	4 - CompChem ready			None	TBD	1.27	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x392_event1	c1c(nc[nH]1)[Br]		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.35	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x393_event2	c1ccc2c(c1)C(C(N2)=O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.74	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x393_event4	c1ccc2c(c1)C(C(N2)=O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.74	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x395_event1	CN1C(C(c2ccccc12)=O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.43	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x396_event2	O=C(O)c1ccccc1C(=O)O		None	3 - Clear density, unexpected ligand	4 - CompChem ready			None	TBD	1.40	P 41 21 2	71 71 149 90 90 90	Save	Save	Save
JMJD2DA-x401_event2	c1cnc2c(c(nc(n2)O)O)n1		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.48	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x402_event1	CC1Nc2ccccc2C(N=1)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.45	P 41 21 2	71 71 149 90 90 90	Save	Save	Save
JMJD2DA-x402_event3	CC1Nc2ccccc2C(N=1)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.45	P 41 21 2	71 71 149 90 90 90	Save	Save	Save
JMJD2DA-x443_event1	C1CC(c2ccc(cc2C1)N)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.34	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x443_event2	C1CC(c2ccc(cc2C1)N)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.34	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x463_event1	c1ccc(c(c1)c1ccccc1O)O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.29	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x486_event1	c1cc(c(cc1[N+]([O-])=O)O)O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.36	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x486_event2	c1cc(c(cc1[N+]([O-])=O)O)O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.36	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x486_event3	c1cc(c(cc1[N+]([O-])=O)O)O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.36	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x494_event1	c1ccc(cc1)c1c[nH]cn1		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.35	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x542_event1	c1ccc(cc1)NC(N)=S		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.39	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x542_event2	c1ccc(cc1)NC(N)=S		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.39	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x542_event3	c1ccc(cc1)NC(N)=S		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.39	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x543_event1	c1cc(ccc1NC(N)=S)F		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.40	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x555_event2	C(CN)c1ccc(c(c1)O)O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.60	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x568_event1	Cc1nc2ccccc2[nH]1		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.97	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x611_event3	c1cc(c(nc1)O)[N+]([O-])=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.15	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x620_event2	c1ccc2c(c1)nc[nH]2		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.25	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x623_event1	c1cc2c(cc1[Cl])C(C(N2)=O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.14	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x637_event1	Cc1ccccc1S(N)(=O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.40	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x637_event4	Cc1ccccc1S(N)(=O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.40	P 41 21 2	71 71 150 90 90 90	Save	Save	Save
JMJD2DA-x639_event2	CC(c1ccc(cc1)O)=O		None	4 - High Confidence	4 - CompChem ready			None	TBD	1.29	P 41 21 2	71 71 150 90 90 90	Save	Save	Save