SMTL ID : 5fzm.1

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid (N09989b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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

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

DMS.2: 8 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 Ligands: P60.16 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210 DMS.3: 11 residues within 4Å: Chain A: Q.65, Q.73, T.74, R.75, V.76, Y.134, S.204, F.205, C.206 Ligands: EDO.15, P60.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.65, A:C.206 DMS.4: 8 residues within 4Å: Chain A: I.209, W.213, E.240, R.293, H.326, Y.327, L.330, R.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.332 Salt bridges: A:E.240

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

MN.5: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: P60.16 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

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

EDO.6: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.9 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.7: 7 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, V.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.135, A:D.137, A:V.198 EDO.8: 4 residues within 4Å: Chain A: R.375, L.441, Y.443, T.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 EDO.9: 6 residues within 4Å: Chain A: R.321, D.339, M.367, E.371, L.374 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.321, A:M.367 EDO.10: 3 residues within 4Å: Chain A: P.7, P.276, V.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.277, A:V.277 EDO.11: 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.12: 3 residues within 4Å: Chain A: G.233, Y.234, R.293 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.233, A:A.236 EDO.13: 5 residues within 4Å: Chain A: R.379, V.383, I.384, D.385, L.441 No protein-ligand interaction detected (PLIP) EDO.14: 8 residues within 4Å: Chain A: Y.134, G.135, Y.197, V.198, G.199, S.203, S.204, N.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.135, A:S.204, A:N.300 Water bridges: A:K.226 EDO.15: 7 residues within 4Å: Chain A: R.75, F.205, C.206, H.208, V.262 Ligands: DMS.3, P60.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.76, A:C.206, A:C.206

1 x P60: 5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid(Non-covalent)

P60.16: 12 residues within 4Å: Chain A: R.75, V.76, A.136, Y.197, F.205, H.208, E.210, H.296 Ligands: DMS.2, DMS.3, MN.5, EDO.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.76, A:A.136, A:F.205 Salt bridges: A:H.208, A:H.296 pi-Stacking: A:Y.197, A:H.208

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

CL.17: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 Ligand excluded by PLIP

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

PO4.18: 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

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 5-(2-Fluorophenyl)-1,3-Oxazole-4-Carboxylic Acid (N09989B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening). To be Published

Release Date

2017-03-29

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