SMTL ID : 6h0x.1

Crystal Structure of KDM4D with tetrazolylhydrazide ligand AA040

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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

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

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

EDO.3: 3 residues within 4Å: Chain A: K.124, K.127, N.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.124, A:N.128 EDO.4: 6 residues within 4Å: Chain A: E.122, P.251, T.252, K.255, F.261, R.263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.251, A:K.255, A:R.263, A:R.263 Water bridges: A:T.252 EDO.5: 10 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, N.202, A.292, I.293, N.294, T.318 Ligands: FJB.7 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.6: 5 residues within 4Å: Chain A: H.192, E.194, S.200, H.280 Ligands: FJB.7 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, FJB.7

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

FJB.7: 21 residues within 4Å: Chain A: L.75, H.90, Y.136, A.138, D.139, Y.181, F.189, H.192, E.194, S.200, N.202, K.210, H.244, K.245, V.246, H.280, N.284, A.290, R.316 Ligands: EDO.5, NI.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.75, A:H.90, A:R.316 Hydrogen bonds: A:Y.136, A:Y.136, A:N.202, A:K.210, A:K.245 Water bridges: A:Y.181, A:E.194, A:T.318, A:T.318, A:T.318 pi-Stacking: A:H.90, 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 AA040. 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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