SMTL ID : 6ett.1

Crystal structure of KDM4D with tetrazole compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.238, F.241, H.244, C.310, C.312, E.314, A.315 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

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

NI.2: 4 residues within 4Å: Chain A: H.192, E.194, S.200, H.280 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.4, H2O.5, H2O.6

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: F.261, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.262, A:N.262

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

EDO.4: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:K.124, A:N.128 EDO.5: 9 residues within 4Å: Chain A: N.29, F.31, T.149, K.150, Q.151, W.152, N.153, H.156, L.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.29, A:W.152, A:N.153, A:N.153 Water bridges: A:F.31 EDO.6: 7 residues within 4Å: Chain A: E.122, P.251, T.252, K.255, F.261, R.263 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 EDO.7: 7 residues within 4Å: Chain A: F.118, E.119, E.122, T.211, R.263, I.264, T.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.264 Water bridges: A:T.265, A:T.265, A:T.265 EDO.8: 9 residues within 4Å: Chain A: K.108, K.109, Y.110, Q.111, T.112, P.113, N.132, W.185, K.186 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.111, A:N.132, A:W.185, A:K.186 Water bridges: A:Q.111 EDO.9: 3 residues within 4Å: Chain A: C.168, K.305, L.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.305 EDO.10: 8 residues within 4Å: Chain A: E.122, R.123, W.126, Y.213, P.251, T.252, R.263 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.123 EDO.11: 7 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, A.292, I.293, N.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.294 Water bridges: A:E.194, A:S.200, A:N.294 EDO.12: 4 residues within 4Å: Chain A: E.27, K.33, Y.34, Y.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27 EDO.13: 7 residues within 4Å: Chain A: I.35, A.36, E.39, Y.199, T.297, P.298, R.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.199, A:T.297, A:R.299 Water bridges: A:A.36 EDO.14: 11 residues within 4Å: Chain A: I.160, N.176, Y.179, D.195, L.198, N.294, V.317, T.318, S.320, M.321, F.324 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.176, A:D.195, A:D.195, A:T.318 Water bridges: A:T.177, A:T.177, A:Y.179, A:N.294

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

SO4.15: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:T.62, A:T.62 Water bridges: A:R.60, A:R.60, A:R.60, A:R.60, A:R.60, A:N.65 Salt bridges: A:R.60 SO4.16: 3 residues within 4Å: Chain A: R.102, H.103, N.106 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.106 Water bridges: A:R.102, A:R.102, A:R.102, A:R.102, A:H.103, A:H.103 Salt bridges: A:R.102, A:H.103 SO4.17: 2 residues within 4Å: Chain A: M.19, I.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.20 Water bridges: A:I.18

1 x BXH: ethyl 2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoate(Non-covalent)

BXH.18: 13 residues within 4Å: Chain A: L.75, Q.77, H.90, Y.136, A.138, D.139, Y.181, T.188, F.189, A.190, H.192, K.210, K.245 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.75, A:Y.136, A:A.138, A:Y.181 Hydrogen bonds: A:K.245 Water bridges: A:A.190, A:N.202, A:N.202, A:K.210, A:K.210 Salt bridges: A:H.90, A:K.245

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

CL.19: 5 residues within 4Å: Chain A: P.113, K.124, N.128, W.185, K.186 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Structure-Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases. Chemmedchem (2019)

Release Date

2019-02-20

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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