SMTL ID : 6etw.1

Crystal structure of KDM4D with tetrazolhydrazide compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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

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

EDO.3: 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:R.123, A:K.124, A:N.128 EDO.4: 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:N.153 Water bridges: A:T.149, A:K.150, A:W.152, A:W.152 EDO.5: 6 residues within 4Å: Chain A: E.122, P.251, T.252, K.255, F.261, R.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.251, A:R.263, A:R.263 Water bridges: A:T.252 EDO.6: 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

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

SO4.7: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 9 PLIP interactions: 9 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:N.65 Salt bridges: A:R.60 SO4.8: 2 residues within 4Å: Chain A: M.19, I.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.20

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

NI.9: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: BX5.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.6

1 x BX5: [4-(2~{H}-1,2,3,4-tetrazol-5-yl)butanoylamino]azanium(Non-covalent)

BX5.10: 16 residues within 4Å: Chain A: Y.136, Y.181, T.187, 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.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.181, A:F.189, A:W.212 Hydrogen bonds: A:S.200, A:N.202, A:N.202, A:K.210, A:N.284 Water bridges: A:Y.136, A:K.245, A:N.294

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain A: R.102, H.103, N.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.102, A:N.106 Water bridges: A:R.102

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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