SMTL ID : 5fzk.1

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 Ligand excluded by PLIP

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

MN.3: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: NRW.13 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.3, H2O.5

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

EDO.4: 5 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411 Water bridges: A:D.339 EDO.5: 7 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, V.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.135, A:D.137, A:V.198 Water bridges: A:D.137, A:I.138 EDO.6: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 EDO.7: 5 residues within 4Å: Chain A: R.321, D.339, M.367, E.371, L.374 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.321, A:E.371 Water bridges: A:D.339, A:D.339 EDO.8: 3 residues within 4Å: Chain A: P.7, V.277, Y.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.277 EDO.9: 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.10: 3 residues within 4Å: Chain A: G.233, Y.234, R.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.293 Water bridges: A:E.237 EDO.11: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 No protein-ligand interaction detected (PLIP) EDO.12: 2 residues within 4Å: Chain A: H.273, E.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.273, A:H.273

1 x NRW: N,3-dimethyl-N-[(pyridin-3-yl)methyl]-1,2-oxazole-5-carboxamide(Non-covalent)

NRW.13: 11 residues within 4Å: Chain A: Q.65, Q.73, R.75, Y.134, Y.197, F.205, C.206, H.208, W.228, H.296 Ligands: MN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.205 Hydrogen bonds: A:C.206 Water bridges: A:Y.197 pi-Stacking: A:F.205

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

PO4.14: 3 residues within 4Å: Chain A: H.331, K.403, H.427 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.331, A:K.403, A:H.427

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

DMS.15: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210 DMS.16: 4 residues within 4Å: Chain A: I.209, W.213, Y.327, L.330 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R. et al., Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment N,3-Dimethyl-N-(Pyridin-3-Ylmethyl)-1,2-Oxazole-5-Carboxamide (N10051A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening). To be Published

Release Date

2016-04-06

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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