SMTL ID : 5fzb.1

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4-Pyridylthiourea (N06275b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, V.309, N.310 Ligands: YS6.16 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210 DMS.4: 9 residues within 4Å: Chain A: Q.65, Q.73, T.74, L.76, Y.134, S.204, F.205, C.206 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206

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

MN.5: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: YS6.16 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.4, H2O.4

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 11 residues within 4Å: Chain A: I.209, W.213, E.240, M.243, L.250, L.261, Y.295, H.326, Y.327, L.330, R.332 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.327 Water bridges: A:W.207, A:Q.260, A:R.332 Salt bridges: A:E.240, A:H.326, A:R.332

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

EDO.7: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.10 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.8: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.135, A:D.137, A:V.198 EDO.9: 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.10: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:M.367 EDO.11: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.233, A:R.293 Water bridges: A:Y.234 EDO.12: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: Q.361, K.362, A.365, I.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.361 EDO.14: 5 residues within 4Å: Chain A: R.75, L.76, C.206, H.208 Ligands: DMS.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.76, A:C.206, A:C.206 Water bridges: A:R.75

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

CL.15: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 Ligand excluded by PLIP

1 x YS6: 1-pyridin-4-ylthiourea(Non-covalent)

YS6.16: 9 residues within 4Å: Chain A: Y.197, F.205, H.208, N.218, K.226, W.228, H.296 Ligands: DMS.3, MN.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.205, A:F.205 Hydrogen bonds: A:K.226 Water bridges: A:N.300

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

PO4.17: 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 PO4.18: 1 residues within 4Å: Chain A: R.388 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.388, A:R.388 Salt bridges: A:R.388

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 Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc -Diamond I04-1 Fragment Screening). To be Published

Release Date

2016-03-30

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B