SMTL ID : 7eqv.1

Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)

DHB.1: 10 residues within 4Å: Chain A: Y.125, Y.170, F.178, H.181, E.183, N.191, K.199, K.234, H.269 Ligands: NI.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.170, A:F.178, A:F.178 Hydrogen bonds: A:Y.125, A:N.191, A:K.234 Water bridges: A:S.281 Salt bridges: A:K.199 DHB.5: 10 residues within 4Å: Chain B: Y.125, Y.170, F.178, H.181, E.183, N.191, K.199, K.234, H.269 Ligands: NI.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.170, B:F.178, B:F.178 Hydrogen bonds: B:N.191, B:K.234 Water bridges: B:S.281 Salt bridges: B:K.199

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

NI.2: 4 residues within 4Å: Chain A: H.181, E.183, H.269 Ligands: DHB.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.181, A:E.183, A:H.269, H2O.1 NI.6: 4 residues within 4Å: Chain B: H.181, E.183, H.269 Ligands: DHB.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.181, B:E.183, B:H.269, H2O.7

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.227, H.233, C.299, C.301 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.227, A:H.233, A:C.299, A:C.301 ZN.7: 4 residues within 4Å: Chain B: C.227, H.233, C.299, C.301 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:H.233, B:C.299, B:C.301

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: F.220, P.221, G.222, S.223 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: F.220, P.221, G.222, S.223 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J.S. et al., Natural product myricetin is a pan-KDM4 inhibitor which with poly lactic-co-glycolic acid formulation effectively targets castration-resistant prostate cancer. J.Biomed.Sci. (2022)

Release Date

2022-05-18

Peptides

Lysine-specific demethylase 4A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lysine-specific demethylase 4A