SMTL ID : 6g5x.1 (1 other biounit)

Crystal Structure of KDM4A with compound YP-02-145

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.234, H.240, C.306, S.307, C.308 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.234, A:H.240, A:C.306, A:C.308

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

NI.2: 1 residues within 4Å: Ligands: CIT.8 No protein-ligand interaction detected (PLIP) NI.3: 1 residues within 4Å: Chain A: H.215 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.215, H2O.9, H2O.10 NI.4: 4 residues within 4Å: Chain A: H.188, E.190, H.276 Ligands: CIT.7 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.4

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

EDO.5: 6 residues within 4Å: Chain A: K.224, C.234, E.235, A.236, F.237, L.238 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.234, A:F.237, A:L.238, A:Y.275, A:Y.275 EDO.6: 2 residues within 4Å: Chain A: R.98, N.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.98, A:N.102

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

CIT.7: 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.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.185 Water bridges: A:K.241, A:S.288, A:S.288, A:S.288 Salt bridges: A:H.188, A:K.206, A:K.206, A:H.276 CIT.8: 4 residues within 4Å: Chain A: E.214, H.215, R.218 Ligands: NI.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.217 Salt bridges: A:H.215, A:R.218

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: S.316, D.318, K.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.318, A:K.333

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
A

Lysine-specific demethylase 4A

Related Entries With Identical Sequence