SMTL ID : 6ete.1

Crystal structure of KDM4D with tetrazolhydrazide compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.238, F.241, H.244, C.310, C.312, E.314 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

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

NI.2: 5 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: EDO.10, BWK.13 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.3, BWK.13 NI.3: 1 residues within 4Å: Chain A: H.156 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.156, H2O.9

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

EDO.4: 5 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 Ligands: SO4.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:K.124, A:K.127, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.152, A:N.153 Water bridges: A:N.29, A:F.31, A:T.149, A:K.150 EDO.6: 6 residues within 4Å: Chain A: E.122, P.251, T.252, K.255, F.261, R.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 Water bridges: A:T.252 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:F.118, A:T.211, A:I.264 Water bridges: A:T.265 EDO.8: 10 residues within 4Å: Chain A: K.108, K.109, Y.110, Q.111, T.112, P.113, N.132, W.185, K.186 Ligands: SO4.11 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:N.132 EDO.9: 3 residues within 4Å: Chain A: R.102, H.103, N.106 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.102 EDO.10: 9 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: NI.2, BWK.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.181, A:N.294 Water bridges: A:N.294

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

SO4.11: 7 residues within 4Å: Chain A: P.113, K.124, N.128, W.185, K.186 Ligands: EDO.4, EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.128, A:W.185 Water bridges: A:K.186 Salt bridges: A:K.186 SO4.12: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:T.62, A:T.62 Water bridges: A:N.65 Salt bridges: A:R.60

1 x BWK: [2-(1-methyl-1,2,3,4-tetrazol-4-ium-5-yl)ethanoylamino]azanium(Covalent)

BWK.13: 14 residues within 4Å: Chain A: Y.181, F.189, H.192, E.194, S.200, N.202, K.210, W.212, T.274, H.280, A.290, A.292 Ligands: NI.2, EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.189, A:W.212 Hydrogen bonds: A:S.200, A:K.210 pi-Stacking: A:Y.181 pi-Cation interactions: A:K.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal structure of KDM4D with tetrazolylhydrazide ligand NR128. To be published

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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