SMTL ID : 5fpa.1

Crystal structure of human KDM4D in complex with 3H,4H-pyrido-3,4-d- pyrimidin-4-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.231, H.237, C.303, C.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.231, A:H.237, A:C.303, A:C.305

1 x CO: COBALT (II) ION(Non-covalent)

CO.2: 4 residues within 4Å: Chain A: H.185, E.187, H.273 Ligands: N5J.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.185, A:E.187, A:H.273, H2O.16, H2O.16

1 x N5J: 3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE(Non-covalent)

N5J.3: 9 residues within 4Å: Chain A: Y.129, Y.174, F.182, H.185, N.195, K.203, W.205, H.273 Ligands: CO.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.182, A:W.205 Hydrogen bonds: A:Y.129, A:N.195 Water bridges: A:S.193 pi-Stacking: A:F.182

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: P.106, K.117, N.121, W.178, K.179 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.117, A:N.121 Water bridges: A:N.125, A:N.125, A:W.178, A:W.178, A:K.179 Salt bridges: A:K.179 SO4.5: 4 residues within 4Å: Chain A: R.53, E.54, T.55, N.58 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.54, A:T.55, A:N.58 Water bridges: A:R.53, A:T.55, A:N.58, A:N.58 Salt bridges: A:R.53 SO4.6: 4 residues within 4Å: Chain A: R.116, K.117, K.120, N.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.121 Salt bridges: A:R.116, A:K.117, A:K.120 SO4.7: 3 residues within 4Å: Chain A: R.95, H.96, N.99 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.99 Water bridges: A:R.95, A:R.95, A:R.95, A:H.96, A:H.96, A:H.96, A:H.96 Salt bridges: A:R.95, A:H.96 SO4.8: 2 residues within 4Å: Chain A: Q.109, N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 SO4.9: 3 residues within 4Å: Chain A: D.295, Y.296, M.299 No protein-ligand interaction detected (PLIP) SO4.10: 7 residues within 4Å: Chain A: Y.172, Y.174, E.187, S.193, A.285, I.286, N.287 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.174, A:Y.174, A:N.287 Water bridges: A:N.287, A:N.287, A:N.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Westaway, S.M. et al., Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. J.Med.Chem. (2016)

Release Date

2016-01-27

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4D

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