SMTL ID : 5ceh.1

Structure of histone lysine demethylase KDM5A in complex with selective inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.473, E.475, H.561 Ligands: 50P.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.473, A:E.475, A:H.561, H2O.1

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.666, A.668, C.669, C.689, H.692 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.666, A:C.669, A:C.689, A:H.692 ZN.3: 5 residues within 4Å: Chain A: C.680, S.681, C.682, C.697, C.699 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.680, A:C.682, A:C.697, A:C.699

1 x 50P: 7-oxo-5-phenyl-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

50P.4: 16 residues within 4Å: Chain A: Y.399, G.400, A.401, Y.462, V.463, S.468, S.469, F.470, H.473, E.475, N.483, K.491, W.493, H.561, N.565 Ligands: NI.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.399, A:Y.399, A:A.401, A:Y.462, A:F.470 Hydrogen bonds: A:N.483, A:N.565 pi-Stacking: A:Y.462, A:Y.462, A:F.470

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinogradova, M. et al., An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells. Nat.Chem.Biol. (2016)

Release Date

2016-05-18

Peptides

Lysine-specific demethylase 5A: A
Unknown Peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase 5A

Unknown Peptide

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