SMTL ID : 6dqd.2 (1 other biounit)

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 i.e. 2-(5-([1,1'-biphenyl]-3-yl)-4-(1-(2-(piperidin-1-yl)ethoxy)ethyl)-1H-pyrazol-1-yl)isonicotinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x H67: 2-[5-([1,1'-biphenyl]-3-yl)-4-{(1S)-1-[2-(piperidin-1-yl)ethoxy]ethyl}-1H-pyrazol-1-yl]pyridine-4-carboxylic acid(Non-covalent)

H67.1: 16 residues within 4Å: Chain A: Q.77, Y.151, A.153, D.154, W.212, Y.214, F.222, C.223, H.225, E.227, N.235, K.243, W.245, H.313 Ligands: MN.2, DMS.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.151, A:A.153, A:W.212, A:Y.214, A:F.222, A:W.245 Hydrogen bonds: A:Y.151 Salt bridges: A:D.154, A:K.243 pi-Stacking: A:F.222, A:H.225 pi-Cation interactions: A:H.225 H67.7: 16 residues within 4Å: Chain B: Q.77, Y.151, A.153, D.154, W.212, Y.214, F.222, C.223, H.225, E.227, N.235, K.243, W.245, H.313 Ligands: MN.8, DMS.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.151, B:A.153, B:W.212, B:Y.214, B:F.222, B:W.245 Salt bridges: B:D.154, B:K.243 pi-Stacking: B:F.222, B:H.225 pi-Cation interactions: B:H.225

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

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: H67.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, A:H.313, H2O.2 MN.8: 4 residues within 4Å: Chain B: H.225, E.227, H.313 Ligands: H67.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.225, B:E.227, B:H.313, H2O.9

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: D.228, H.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.229 GOL.4: 6 residues within 4Å: Chain A: L.82, V.140, S.141, I.281, M.282, N.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.140, A:N.283 GOL.9: 2 residues within 4Å: Chain B: D.228, H.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.229 Water bridges: B:H.229 GOL.10: 6 residues within 4Å: Chain B: L.82, V.140, S.141, I.281, M.282, N.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.140, B:N.283

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

DMS.5: 5 residues within 4Å: Chain A: Y.214, E.227, S.233, N.327 Ligands: H67.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.214 Salt bridges: A:E.227 DMS.6: 3 residues within 4Å: Chain A: S.250, P.309, R.310 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain B: Y.214, E.227, S.233, N.327 Ligands: H67.7 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.227 DMS.12: 3 residues within 4Å: Chain B: S.250, P.309, R.310 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., To be determined. To Be Published

Release Date

2019-06-12

Peptides

Linked KDM5A Jmj Domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Linked KDM5A Jmj Domain

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