SMTL ID : 6ej0.1

Crystal structure of KDM5B in complex with KDOPZ000049a.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.396, C.399, C.419, H.422 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.396, A:C.399, A:C.419, A:H.422

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: L.66, N.67, L.117, V.118, T.120, E.123 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.117, A:T.120, H2O.1 MN.10: 4 residues within 4Å: Chain A: H.203, E.205, H.291 Ligands: B7K.11 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.203, A:E.205, A:H.291, H2O.1, H2O.3

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

EDO.3: 5 residues within 4Å: Chain A: D.334, C.403, F.404, M.405, S.406 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.334, A:F.404, A:M.405, A:S.406, A:S.406 Water bridges: A:D.334 EDO.4: 3 residues within 4Å: Chain A: G.228, Y.229, L.314 No protein-ligand interaction detected (PLIP)

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: I.204, W.208, E.235, R.288, H.321, Y.322, L.325, R.327 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.235 DMS.6: 7 residues within 4Å: Chain A: W.190, Y.192, E.205, S.211, A.303, V.304, N.305 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.205 DMS.7: 8 residues within 4Å: Chain A: F.59, G.130, A.131, D.132, F.138, L.191, Y.192, V.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.132 Salt bridges: A:D.132 pi-Cation interactions: A:F.138 DMS.8: 6 residues within 4Å: Chain A: E.335, K.339, S.342, E.387, F.404, Y.440 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.342, A:Y.440 Water bridges: A:R.439 Salt bridges: A:E.387 DMS.9: 2 residues within 4Å: Chain A: H.326, H.422 No protein-ligand interaction detected (PLIP)

1 x B7K: 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

B7K.11: 15 residues within 4Å: Chain A: R.62, R.74, Y.129, G.130, W.190, Y.192, S.199, F.200, H.203, N.213, K.221, W.223, H.291, N.295 Ligands: MN.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.129, A:W.190, A:Y.192, A:Y.192 Hydrogen bonds: A:R.62, A:N.213, A:N.295 Water bridges: A:H.203, A:K.221 pi-Stacking: A:Y.192, A:Y.192, A:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

srikannathasan, v., Crystal structure of KDM5B in complex with KDOPZ000049a. to be published

Release Date

2018-05-02

Peptides

Lysine-specific demethylase 5B,Lysine-specific demethylase 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5B,Lysine-specific demethylase 5B