SMTL ID : 5fp9.1

Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 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 ZN.12: 4 residues within 4Å: Chain B: C.231, H.237, C.303, C.305 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.231, B:H.237, B:C.303, B:C.305

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

CO.2: 4 residues within 4Å: Chain A: H.185, E.187, H.273 Ligands: 4SV.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.185, A:E.187, A:H.273, H2O.15, H2O.15 CO.13: 4 residues within 4Å: Chain B: H.185, E.187, H.273 Ligands: 4SV.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.185, B:E.187, B:H.273, H2O.36, H2O.36

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: F.24, K.143, Q.144, W.145, N.146, H.149, L.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.24, A:W.145, A:N.146, A:N.146 Water bridges: A:D.25 GOL.14: 7 residues within 4Å: Chain B: F.24, K.143, Q.144, W.145, N.146, H.149, L.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.24, B:W.145, B:N.146, B:N.146 Water bridges: B:D.25

2 x 4SV: 3-AMINOPYRIDINE-4-CARBOXYLIC ACID(Non-covalent)

4SV.4: 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.182, A:F.182, A:W.205 Hydrogen bonds: A:N.195 Water bridges: A:D.132, A:S.193 Salt bridges: A:K.203 4SV.15: 9 residues within 4Å: Chain B: Y.129, Y.174, F.182, H.185, N.195, K.203, W.205, H.273 Ligands: CO.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.182, B:F.182, B:W.205 Hydrogen bonds: B:Y.129, B:N.195 Water bridges: B:D.132, B:S.193 Salt bridges: B:K.203

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

SO4.5: 6 residues within 4Å: Chain A: P.106, K.117, N.121, N.125, W.178, K.179 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.117, A:N.121 Water bridges: A:N.125, A:N.125, A:W.178 Salt bridges: A:K.179 SO4.6: 4 residues within 4Å: Chain A: R.53, E.54, T.55, N.58 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.54, A:T.55, A:N.58 Water bridges: A:T.55, A:T.55, B:E.158, B:E.158, B:E.158 Salt bridges: A:R.53 SO4.7: 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 SO4.8: 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:H.96, A:H.96, A:H.96, A:H.96, A:H.96 Salt bridges: A:R.95, A:H.96 SO4.9: 2 residues within 4Å: Chain A: Q.109, N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 SO4.10: 3 residues within 4Å: Chain A: D.295, Y.296, M.299 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.295, A:Y.296 SO4.11: 6 residues within 4Å: Chain A: Y.172, Y.174, E.187, A.285, I.286, N.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.174, A:Y.174, A:N.287 Water bridges: A:N.287, A:N.287 SO4.16: 6 residues within 4Å: Chain B: P.106, K.117, N.121, N.125, W.178, K.179 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.117, B:N.121 Water bridges: B:N.125, B:N.125, B:W.178 Salt bridges: B:K.179 SO4.17: 4 residues within 4Å: Chain B: R.53, E.54, T.55, N.58 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.54, B:T.55, B:N.58 Water bridges: B:T.55 Salt bridges: B:R.53 SO4.18: 4 residues within 4Å: Chain B: R.116, K.117, K.120, N.121 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.121 Salt bridges: B:R.116, B:K.117, B:K.120 SO4.19: 3 residues within 4Å: Chain B: R.95, H.96, N.99 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.99 Water bridges: B:R.95, B:R.95, B:H.96, B:H.96, B:H.96, B:H.96 Salt bridges: B:R.95, B:H.96 SO4.20: 2 residues within 4Å: Chain B: Q.109, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 SO4.21: 3 residues within 4Å: Chain B: D.295, Y.296, M.299 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.296, B:Y.296, B:Y.296 SO4.22: 6 residues within 4Å: Chain B: Y.172, Y.174, E.187, A.285, I.286, N.287 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.174, B:N.287 Water bridges: B:N.287, B: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

HUMAN LYSINE-SPECIFIC DEMETHYLASE 4D JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D, JMJD2D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HUMAN LYSINE-SPECIFIC DEMETHYLASE 4D JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D, JMJD2D

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