SMTL ID : 6etv.1

Crystal structure of KDM4D with tetrazolhydrazide compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 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 CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: P.113, K.124, N.128, W.185, K.186 Ligand excluded by PLIP

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

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

EDO.4: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:K.124, A:N.128 Water bridges: A:R.123 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.29, A:W.152, A:N.153 Water bridges: A:F.31, A:T.149, A:H.156 EDO.6: 6 residues within 4Å: Chain A: E.122, P.251, T.252, K.255, F.261, R.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 EDO.7: 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.8: 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.9: 8 residues within 4Å: Chain A: F.118, E.119, E.122, T.211, R.263, I.264, T.265, H.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.265 Water bridges: A:T.265, A:T.265, A:T.265 EDO.10: 4 residues within 4Å: Chain A: E.27, K.33, Y.34, Y.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.27 Water bridges: A:K.33

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

SO4.11: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:T.62, A:T.62, A:N.65 Water bridges: A:R.60, A:R.60, A:R.60, A:R.60 Salt bridges: A:R.60

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

NI.12: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: BXE.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.4

1 x BXE: [3-(2~{H}-1,2,3,4-tetrazol-5-yl)propanoylamino]azanium(Non-covalent)

BXE.13: 15 residues within 4Å: Chain A: Y.136, Y.181, F.189, H.192, E.194, S.200, N.202, K.210, W.212, T.274, H.280, N.284, A.290, A.292 Ligands: NI.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.189, A:W.212 Hydrogen bonds: A:E.194, A:N.202, A:N.202, A:K.210 Water bridges: A:N.284, A:N.284, A:A.290, A:N.294 pi-Stacking: A:Y.181, A:F.189

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: R.102, H.103, N.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.102, A:R.102, A:N.106 Water bridges: A:H.103, A:H.103

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.15: 2 residues within 4Å: Chain A: K.255, E.256 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.255, A:K.255 Salt bridges: A:K.255

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

2019-02-27

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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