SMTL ID : 6h11.1

Crystal Structure of KDM4D with tetrazolylhydrazide ligand AA028

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 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

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

EDO.3: 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.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, A:N.153 Water bridges: A:F.31, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 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 EDO.7: 9 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, A.292, I.293, N.294, T.318 Ligands: FHT.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.318, A:T.318 Water bridges: A:Y.181, A:Y.181, A:N.294

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

NI.8: 5 residues within 4Å: Chain A: H.192, E.194, S.200, H.280 Ligands: FHT.9 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.6, FHT.9

1 x FHT: [[(2~{R})-2-[(4-bromophenyl)carbonylamino]-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoyl]amino]azanium(Non-covalent)

FHT.9: 19 residues within 4Å: Chain A: L.75, H.90, Y.136, A.138, D.139, Y.181, F.189, A.190, H.192, E.194, S.200, N.202, K.210, K.245, H.280, A.290, A.292 Ligands: EDO.7, NI.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.138 Hydrogen bonds: A:Y.136, A:Y.136, A:E.194, A:N.202, A:K.210, A:K.245 Water bridges: A:Y.181, A:Y.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazolylhydrazide ligand AA028. To be published

Release Date

2020-01-29

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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