SMTL ID : 6ein.1

Crystal structure of KDM5B in complex with S49365a.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x B7Z: 8-[4-[2-(4-propanoylpiperazin-1-yl)ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Covalent)

B7Z.1: 14 residues within 4Å: Chain A: Y.134, D.137, C.189, G.190, W.195, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296 Ligands: MN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.228 Hydrogen bonds: A:Y.134, A:Y.134, A:N.218 Water bridges: A:N.310 Salt bridges: A:D.137 pi-Stacking: A:F.205, A:F.205

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.401, C.404, C.424, H.427 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.401, A:C.404, A:C.424, A:H.427

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

MN.3: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: B7Z.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.3 MN.4: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP)

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

EDO.5: 8 residues within 4Å: Chain A: P.174, S.179, L.181, M.191, K.192, N.310, F.311, C.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.179, A:L.181, A:M.191, A:C.312 EDO.6: 7 residues within 4Å: Chain A: I.209, W.213, R.293, H.326, Y.327, L.330, R.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.213, A:H.326, A:R.332 Water bridges: A:Y.327, A:R.332 EDO.7: 6 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:M.367 EDO.8: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

srikannathasan, v., Crystal structure of KDM5B in complex with S49365a. 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

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