SMTL ID : 5a3n.1

Crystal structure of human PLU-1 (JARID1B) in complex with KDOAM25a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.67, A:L.122, A:T.125, A:E.128 MN.4: 1 residues within 4Å: Chain A: E.387 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.387, H2O.16 MN.5: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: LQT.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.9

1 x LQT: 2-[[[2-[2-(dimethylamino)ethyl-ethyl-amino]-2-oxidanylidene-ethyl]amino]methyl]pyridine-4-carboxamide(Non-covalent)

LQT.6: 16 residues within 4Å: Chain A: R.75, Y.134, W.195, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296, A.308, V.309, N.310 Ligands: MN.5, DMS.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.197, A:F.205, A:W.228 Hydrogen bonds: A:R.75, A:Y.134, A:Y.134 Water bridges: A:N.310 pi-Stacking: A:F.205

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

DMS.7: 5 residues within 4Å: Chain A: R.75, V.76, Y.134, Y.197 Ligands: LQT.6 No protein-ligand interaction detected (PLIP)

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

PO4.8: 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

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

EPE.9: 13 residues within 4Å: Chain A: I.209, W.213, E.240, M.243, L.250, F.251, L.261, V.262, Y.295, H.326, Y.327, L.330, R.332 10 PLIP interactions: 10 interactions with chain A Water bridges: A:W.207, A:W.213, A:E.240, A:L.261, A:L.261, A:Y.327 Salt bridges: A:E.240, A:H.326, A:R.332 pi-Cation interactions: A:F.251

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

EDO.10: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.397, A:Q.400, A:V.402, A:L.422, A:L.422 EDO.11: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.379, A:R.379 EDO.12: 8 residues within 4Å: Chain A: A.95, D.96, K.99, M.200, C.201, E.224, G.302, F.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.96, A:C.201, A:E.224, A:F.303 EDO.13: 6 residues within 4Å: Chain A: F.51, A.52, C.53, G.144, S.145, F.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.52, A:G.144 EDO.14: 2 residues within 4Å: Chain A: M.389, L.422 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.420 EDO.15: 2 residues within 4Å: Chain A: E.387, K.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.440 Water bridges: A:S.416, A:K.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumber, A. et al., Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol (2017)

Release Date

2015-07-08

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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