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

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N67 i.e. 2-(5-phenyl-4-(phenyl(2-(piperidin-1-yl)ethoxy)methyl)-1H-pyrazol-1-yl)isonicotinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x H6A: 2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid(Non-covalent)

H6A.1: 16 residues within 4Å: Chain A: R.75, Y.151, A.153, D.154, W.212, Y.214, F.222, H.225, E.227, K.243, W.245, Q.277, L.278, H.313 Ligands: MN.2, DMS.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.153, A:Y.214, A:F.222, A:H.225, A:W.245, A:L.278 Hydrogen bonds: A:Y.151 Salt bridges: A:D.154, A:K.243 pi-Stacking: A:Y.214, A:F.222, A:H.225 pi-Cation interactions: A:H.225 H6A.7: 16 residues within 4Å: Chain B: R.75, Y.151, A.153, D.154, W.212, Y.214, F.222, H.225, E.227, K.243, W.245, Q.277, L.278, H.313 Ligands: MN.8, DMS.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.153, B:Y.214, B:F.222, B:H.225, B:W.245, B:L.278 Salt bridges: B:D.154, B:K.243 pi-Stacking: B:Y.214, 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: H6A.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.6 MN.8: 4 residues within 4Å: Chain B: H.225, E.227, H.313 Ligands: H6A.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.15

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.227, D.228, H.229, W.230, L.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227, A:H.229 Water bridges: A:Q.277 GOL.9: 5 residues within 4Å: Chain B: E.227, D.228, H.229, W.230, L.274 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.227, B:D.228, B:H.229 Water bridges: B:H.229, B:Q.277

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

DMS.4: 6 residues within 4Å: Chain A: L.256, E.257, M.260, D.273, H.276, Y.312 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.273 DMS.5: 6 residues within 4Å: Chain A: W.212, Y.214, E.227, A.325, N.327 Ligands: H6A.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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.250 DMS.10: 6 residues within 4Å: Chain B: L.256, E.257, M.260, D.273, H.276, Y.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.312 Water bridges: B:D.273 Salt bridges: B:D.273 DMS.11: 6 residues within 4Å: Chain B: W.212, Y.214, E.227, A.325, N.327 Ligands: H6A.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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.250

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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