SMTL ID : 5a3t.1

Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl) isonicotinic acid).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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 EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 14 residues within 4Å: Chain A: I.209, W.213, E.240, M.243, L.250, F.251, L.261, V.262, R.293, Y.295, H.326, Y.327, L.330, R.332 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.213 Water bridges: A:L.261, A:T.263 Salt bridges: A:E.240, A:R.293, A:H.326, A:R.332 pi-Cation interactions: A:F.251

1 x MMK: 2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4-CARBOXYLIC ACID(Non-covalent)

MMK.3: 16 residues within 4Å: Chain A: R.75, Y.134, D.137, 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.12 10 PLIP interactions: 10 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.197 Water bridges: A:N.310 Salt bridges: A:D.137, A:K.226 pi-Stacking: A:F.205

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

NI.4: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411 EDO.6: 3 residues within 4Å: Chain A: R.375, L.441, T.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 EDO.7: 9 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, I.126, E.128, D.129, V.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.67, A:V.130, A:V.130 Water bridges: A:N.68, A:V.123 EDO.8: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:M.367 EDO.9: 8 residues within 4Å: Chain A: P.174, S.179, L.181, M.191, K.192, N.310, F.311, C.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.312, A:C.312 EDO.10: 10 residues within 4Å: Chain A: E.177, S.179, V.180, L.181, A.182, H.183, I.184, M.345, L.352, V.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.177, A:H.183, A:I.184 EDO.11: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.398, A:Q.400, A:L.422

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

MN.12: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: MMK.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. (2016)

Release Date

2015-06-17

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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