SMTL ID : 6etg.1

Crystal structure of KDM4D with tetrazolhydrazide compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 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: 5 residues within 4Å: Chain A: H.192, E.194, S.200, H.280 Ligands: BWT.15 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.8

9 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.29, A:N.153 Water bridges: A:F.31, 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: 7 residues within 4Å: Chain A: F.118, E.119, E.122, T.211, R.263, I.264, T.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.264 Water bridges: A:T.265 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: 8 residues within 4Å: Chain A: F.31, D.32, I.35, L.157, G.158, F.295, A.296, T.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.32, A:D.32, A:G.158, A:G.158 Water bridges: A:A.296 EDO.9: 8 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: BWT.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.181, A:E.194, A:N.294 Water bridges: A:S.200 EDO.10: 5 residues within 4Å: Chain A: K.25, P.54, E.56, W.57, Q.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151 EDO.11: 9 residues within 4Å: Chain A: I.160, N.176, D.195, L.198, N.294, T.318, S.320, M.321, F.324 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.195, A:D.195 Water bridges: A:N.176, A:N.176, A:N.294

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

SO4.12: 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 SO4.13: 3 residues within 4Å: Chain A: R.102, H.103, N.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.102, A:N.106 Water bridges: A:R.102, A:H.103, A:H.103 Salt bridges: A:H.103 SO4.14: 1 residues within 4Å: Chain A: K.255 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.255

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

BWT.15: 15 residues within 4Å: Chain A: Q.77, Y.136, T.187, T.188, F.189, H.192, E.194, S.200, N.202, K.210, K.245, H.280, N.284 Ligands: NI.2, EDO.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.189, A:F.189, A:F.189 Hydrogen bonds: A:Q.77, A:Q.77, A:Y.136, A:E.194, A:N.284

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

NA.16: 3 residues within 4Å: Chain A: N.17, F.261, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.261, A:N.262

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

CL.17: 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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