SMTL ID : 6g5w.2 (1 other biounit)

Crystal Structure of KDM4A with compound YP-03-038

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.234, H.240, C.306, C.308 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.234, A:H.240, A:C.306, A:C.308

2 x NI: NICKEL (II) ION(Non-covalent)(Non-functional Binders)

NI.2: 4 residues within 4Å: Chain A: H.188, E.190, H.276 Ligands: CIT.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.188, A:E.190, A:H.276, H2O.1, H2O.2 NI.3: 1 residues within 4Å: Ligands: ENZ.7 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: N.26, S.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.26, A:S.28 Water bridges: A:S.28

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: Y.59, D.60, R.98, F.202, F.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.59, A:D.60, A:R.98

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 11 residues within 4Å: Chain A: Y.132, Y.177, F.185, H.188, N.198, K.206, W.208, H.276, A.286, S.288 Ligands: NI.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.177, A:F.185 Water bridges: A:K.241, A:K.241, A:S.288, A:S.288 Salt bridges: A:H.188, A:K.206, A:K.206, A:H.276

1 x ENZ: (4~{R})-5-methyl-4-phenyl-2-pyridin-2-yl-pyrazolidin-3-one(Non-covalent)

ENZ.7: 10 residues within 4Å: Chain A: F.114, E.115, E.118, S.207, W.208, Y.209, K.259, V.260, T.261 Ligands: NI.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.114, A:E.115, A:E.118, A:E.118, A:Y.209, A:K.259, A:K.259 Water bridges: A:F.114, A:T.261 pi-Cation interactions: A:K.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carter, D.M. et al., Enhanced Properties of a Benzimidazole Benzylpyrazole Lysine Demethylase Inhibitor: Mechanism-of-Action, Binding Site Analysis, and Activity in Cellular Models of Prostate Cancer. J.Med.Chem. (2021)

Release Date

2019-04-10

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Lysine-specific demethylase 4A

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