SMTL ID : 6h50.1

Crystal structure of human KDM5B in complex with compound 34a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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 ZN.2: 4 residues within 4Å: Chain A: C.415, C.417, C.432, C.434 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.415, A:C.417, A:C.432, A:C.434

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

MN.3: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.122, A:T.125, A:E.128, H2O.6 MN.4: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: FO2.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.1

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

EDO.5: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.135, A:V.198 Water bridges: A:H.59, A:D.137, A:S.140, A:S.140 EDO.6: 5 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 Ligands: DMS.14 No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: R.388 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.388, A:R.388, A:Y.443

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain A: H.331, K.403, H.427 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.331, A:H.427

1 x FO2: 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

FO2.9: 12 residues within 4Å: Chain A: V.76, W.195, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296 Ligands: MN.4, DMS.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.228 Hydrogen bonds: A:N.218 Water bridges: A:D.211, A:D.211 pi-Stacking: A:F.205, A:H.208

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

DMS.10: 8 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 Ligands: FO2.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210 DMS.11: 7 residues within 4Å: Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206 DMS.12: 3 residues within 4Å: Chain A: V.107, H.108, E.224 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.224 Salt bridges: A:D.96, A:E.224 pi-Cation interactions: A:H.108 DMS.13: 8 residues within 4Å: Chain A: E.340, C.343, K.344, S.347, E.392, F.409, R.444, Y.445 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.445 Salt bridges: A:E.392 DMS.14: 6 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.375 pi-Cation interactions: A:Y.443

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le Bihan, Y.V. et al., C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem. (2019)

Release Date

2019-06-12

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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