SMTL ID : 6h4z.1

Crystal structure of human KDM5B in complex with compound 16a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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

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

MN.3: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: FQ5.5 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 MN.4: 5 residues within 4Å: Chain A: L.67, N.68, L.122, 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.2 MN.22: 1 residues within 4Å: Chain A: D.339 No protein-ligand interaction detected (PLIP)

2 x FQ5: 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

FQ5.5: 16 residues within 4Å: Chain A: R.75, Y.134, D.137, C.189, W.195, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296 Ligands: MN.3, DMS.7, DMS.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.137, A:W.195, A:W.228 Hydrogen bonds: A:Y.134, A:Y.134, A:N.218 Salt bridges: A:D.137 pi-Stacking: A:F.205 FQ5.6: 7 residues within 4Å: Chain A: E.8, P.10, I.32, Q.35, T.36, Y.234, Y.278 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.10, A:T.36, A:Y.234 Hydrogen bonds: A:Q.35 pi-Stacking: A:Y.234

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

DMS.7: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, N.310 Ligands: FQ5.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210 DMS.8: 7 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327, L.330, R.332 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.326 Water bridges: A:Y.327 Salt bridges: A:E.240 DMS.9: 7 residues within 4Å: Chain A: E.340, C.343, K.344, E.392, F.409, R.444, Y.445 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.445 Water bridges: A:R.444 Salt bridges: A:E.392 DMS.10: 3 residues within 4Å: Chain A: G.420, L.421, L.422 No protein-ligand interaction detected (PLIP) DMS.11: 7 residues within 4Å: Chain A: R.75, F.205, C.206, H.208, V.262 Ligands: FQ5.5, DMS.12 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.208 DMS.12: 7 residues within 4Å: Chain A: Q.65, Q.73, T.74, S.204, F.205, C.206 Ligands: DMS.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.65, A:C.206 DMS.13: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.375 pi-Cation interactions: A:Y.443 DMS.14: 4 residues within 4Å: Chain A: E.430, L.431, C.432, S.433 No protein-ligand interaction detected (PLIP) DMS.15: 1 residues within 4Å: Chain A: H.108 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.108 Salt bridges: A:D.96 pi-Cation interactions: A:H.108

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

EDO.16: 5 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411 EDO.17: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.293 Water bridges: A:G.233 EDO.18: 3 residues within 4Å: Chain A: H.331, K.403, H.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.331 EDO.19: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.397, A:Q.400, A:L.422, A:L.422 EDO.20: 3 residues within 4Å: Chain A: M.2, L.4, N.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.268 EDO.21: 6 residues within 4Å: Chain A: D.211, Q.260, Y.327, R.332, Y.333 Ligands: DMS.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.211, A:R.332

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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