SMTL ID : 6eiy.1

Crystal structure of KDM5B in complex with KDOPZ000034a.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.399, C.402, C.422, H.425 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.399, A:C.402, A:C.422, A:H.425

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

MN.2: 6 residues within 4Å: Chain A: L.66, N.67, L.120, V.121, T.123, E.126 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.120, A:T.123, A:E.126 MN.9: 4 residues within 4Å: Chain A: H.206, E.208, H.294 Ligands: B6W.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.206, A:E.208, A:H.294, H2O.3, H2O.4

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

EDO.3: 5 residues within 4Å: Chain A: D.337, C.406, F.407, M.408, S.409 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.337, A:F.407, A:M.408, A:S.409, A:S.409 Water bridges: A:D.337 EDO.4: 4 residues within 4Å: Chain A: G.231, Y.232, R.291, L.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.291 Water bridges: A:Y.232, A:P.290 EDO.5: 7 residues within 4Å: Chain A: F.59, G.133, A.134, D.135, L.194, Y.195, V.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.135, A:V.196

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

DMS.6: 7 residues within 4Å: Chain A: I.207, W.211, E.238, H.324, Y.325, L.328, R.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.324 Salt bridges: A:E.238 DMS.7: 7 residues within 4Å: Chain A: W.193, Y.195, E.208, S.214, A.306, V.307, N.308 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.208 DMS.8: 2 residues within 4Å: Chain A: H.329, H.425 No protein-ligand interaction detected (PLIP)

1 x B6W: 2-chloranyl-~{N}-[2-[4-(3-cyano-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidin-5-yl)pyrazol-1-yl]ethyl]ethanamide(Non-covalent)

B6W.10: 21 residues within 4Å: Chain A: Q.64, Q.72, T.73, R.74, V.75, Y.132, G.133, Y.195, V.196, S.201, S.202, F.203, C.204, H.206, N.216, K.224, W.226, V.260, H.294, N.298 Ligands: MN.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.132, A:Y.195, A:F.203 Hydrogen bonds: A:T.73, A:Y.195, A:C.204, A:N.216, A:N.298 Water bridges: A:Y.195, A:K.224 pi-Stacking: A:Y.195, A:Y.195, A:F.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

srikannathasan, v., Crystal structure of KDM5B in complex with KDOPZ000034a. 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