SMTL ID : 6ek6.1

Crystal structure of KDM5B in complex with S49195a.

Coordinates

PDB Format Compare

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.393, C.396, C.416, H.419 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.393, A:C.396, A:C.416, A:H.419

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

MN.2: 6 residues within 4Å: Chain A: L.66, N.67, L.114, V.115, T.117, E.120 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.66, A:L.114, A:T.117, A:E.120, H2O.2

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 4 residues within 4Å: Chain A: H.200, E.202, H.288 Ligands: 90V.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.200, A:E.202, A:H.288, H2O.2

1 x 90V: N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide(Non-covalent)

90V.4: 15 residues within 4Å: Chain A: Y.126, Y.189, S.196, F.197, H.200, E.202, N.210, K.218, W.220, H.288, N.292, A.300, V.301, N.302 Ligands: NI.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.126, A:Y.189, A:Y.189, A:Y.189, A:A.300 Hydrogen bonds: A:N.292 Water bridges: A:S.208, A:K.218

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

DMS.5: 5 residues within 4Å: Chain A: I.201, W.205, H.318, Y.319, L.322 No protein-ligand interaction detected (PLIP) DMS.6: 6 residues within 4Å: Chain A: R.367, S.378, L.433, Y.435, T.438 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.367 pi-Cation interactions: A:Y.435 DMS.7: 2 residues within 4Å: Chain A: H.323, H.419 No protein-ligand interaction detected (PLIP) DMS.8: 2 residues within 4Å: Chain A: V.99, H.100 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.88 pi-Cation interactions: A:H.100

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

EDO.9: 8 residues within 4Å: Chain A: V.316, Y.319, R.320, R.324, C.326, C.396, K.397, T.398 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.396 EDO.10: 5 residues within 4Å: Chain A: D.331, C.400, F.401, M.402, S.403 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.331, A:F.401, A:M.402, A:S.403, A:S.403 Water bridges: A:D.331 EDO.11: 6 residues within 4Å: Chain A: Q.72, S.196, F.197, C.198, H.200, V.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.64, A:Y.126, A:C.198, A:H.200 EDO.12: 6 residues within 4Å: Chain A: R.313, D.331, M.359, D.362, E.363, L.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.313, A:E.363 EDO.13: 5 residues within 4Å: Chain A: R.371, V.375, I.376, L.433 Ligands: DMS.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.371 EDO.14: 1 residues within 4Å: Chain A: R.380 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.380 Water bridges: A:Y.435 EDO.15: 8 residues within 4Å: Chain A: D.389, E.390, R.391, Q.392, V.394, G.412, L.413, L.414 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.389, A:Q.392, A:L.414, A:L.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srikannathasan, V., Crystal structure of KDM5B in complex with S49195a. To be published

Release Date

2018-03-14

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