SMTL ID : 5fp4.1

Crystal structure of human KDM4D in complex with 3-(4- phenylbutanamido)pyridine-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.14: 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 FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: H.185, E.187, H.273 Ligands: YC8.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.185, A:E.187, A:H.273, H2O.12, H2O.13 FE2.15: 4 residues within 4Å: Chain B: H.185, E.187, H.273 Ligands: YC8.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.185, B:E.187, B:H.273, H2O.30, H2O.30

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.14, H.15, P.16, E.20, Y.27, Y.30 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.15, A:E.20, A:Y.27, A:Y.27 Water bridges: A:H.15, A:H.15, A:T.17 GOL.4: 8 residues within 4Å: Chain A: N.22, F.24, K.143, Q.144, W.145, N.146, H.149, L.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.24, A:W.145, A:N.146 Water bridges: A:D.23, A:D.25, A:T.142, A:K.143 GOL.5: 4 residues within 4Å: Chain A: F.111, R.256, I.257, T.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.258 Water bridges: A:K.43 GOL.16: 6 residues within 4Å: Chain B: F.14, H.15, P.16, E.20, Y.27, Y.30 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.15, B:E.20, B:Y.27, B:Y.27 Water bridges: B:T.17 GOL.17: 8 residues within 4Å: Chain B: N.22, F.24, K.143, Q.144, W.145, N.146, H.149, L.150 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.24, B:W.145, B:N.146 Water bridges: B:D.23, B:D.25, B:T.142, B:K.143 GOL.18: 4 residues within 4Å: Chain B: F.111, R.256, I.257, T.258 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.258, B:T.258 Water bridges: B:K.43

2 x YC8: 3-(4-PHENYLBUTANOYLAMINO)PYRIDINE-4-CARBOXYLIC ACID(Non-covalent)

YC8.6: 13 residues within 4Å: Chain A: L.68, H.83, Y.129, D.132, Y.174, F.182, H.185, N.195, K.203, W.205, K.238, H.273 Ligands: FE2.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.68, A:Y.129, A:Y.174, A:F.182, A:W.205, A:K.238 Hydrogen bonds: A:N.195, A:K.238 Salt bridges: A:K.203 pi-Stacking: A:H.83, A:F.182 YC8.19: 13 residues within 4Å: Chain B: L.68, H.83, Y.129, D.132, Y.174, F.182, H.185, N.195, K.203, W.205, K.238, H.273 Ligands: FE2.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.68, B:Y.129, B:Y.174, B:F.182, B:W.205, B:K.238 Hydrogen bonds: B:Y.129, B:N.195, B:K.238 Salt bridges: B:K.203 pi-Stacking: B:H.83, B:F.182

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

SO4.7: 5 residues within 4Å: Chain A: P.106, K.117, N.121, W.178, K.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.121 Water bridges: A:N.125, A:N.125, A:W.178 Salt bridges: A:K.179 SO4.8: 4 residues within 4Å: Chain A: R.53, E.54, T.55, N.58 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.54, A:T.55, A:N.58 Water bridges: A:R.53, A:R.53, A:T.55 Salt bridges: A:R.53 SO4.9: 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 SO4.10: 3 residues within 4Å: Chain A: R.95, H.96, N.99 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.99 Water bridges: A:R.95, A:H.96, A:H.96, A:H.96, A:H.96 Salt bridges: A:R.95, A:H.96 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:E.187 Water bridges: A:N.287, A:N.287 SO4.12: 5 residues within 4Å: Chain A: Q.109, N.110 Chain B: Q.109, N.110 Ligands: SO4.25 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.109, A:Q.109, A:N.110, B:Q.109, B:N.110 SO4.13: 3 residues within 4Å: Chain A: D.295, Y.296, M.299 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.295 SO4.20: 5 residues within 4Å: Chain B: P.106, K.117, N.121, W.178, K.179 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.121 Water bridges: B:N.125, B:N.125, B:W.178 Salt bridges: B:K.179 SO4.21: 4 residues within 4Å: Chain B: R.53, E.54, T.55, N.58 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.54, B:T.55, B:N.58 Water bridges: B:R.53, B:T.55, B:D.57 Salt bridges: B:R.53 SO4.22: 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 SO4.23: 3 residues within 4Å: Chain B: R.95, H.96, N.99 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.99 Water bridges: B:R.95, B:H.96, B:H.96, B:H.96 Salt bridges: B:R.95, B:H.96 SO4.24: 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:E.187 Water bridges: B:N.287, B:N.287 SO4.25: 5 residues within 4Å: Chain A: Q.109, N.110 Chain B: Q.109, N.110 Ligands: SO4.12 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.109, A:N.110, B:Q.109, B:Q.109, B:N.110 SO4.26: 3 residues within 4Å: Chain B: D.295, Y.296, M.299 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSINE-SPECIFIC DEMETHYLASE 4D

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