SMTL ID : 6dq4.2 (1 other biounit)

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR GSK-J1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

2 x K0I: 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid(Non-covalent)

K0I.1: 16 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, D.154, Y.214, F.222, H.225, E.227, N.235, K.243, L.278, A.323 Ligands: MN.2, GOL.5, DMS.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.151, A:A.153, A:Y.214, A:Y.214, A:F.222, A:L.278 Hydrogen bonds: A:Y.151, A:N.235 Water bridges: A:E.227, A:H.313 Salt bridges: A:K.243 pi-Cation interactions: A:R.75 K0I.13: 16 residues within 4Å: Chain B: R.75, Q.77, Y.151, A.153, D.154, Y.214, F.222, H.225, E.227, N.235, K.243, L.278, A.323 Ligands: MN.14, GOL.17, DMS.23 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.151, B:A.153, B:Y.214, B:Y.214, B:F.222, B:L.278 Hydrogen bonds: B:Y.151, B:Y.151, B:Y.214, B:N.235 Water bridges: B:E.227, B:H.313 Salt bridges: B:K.243 pi-Cation interactions: B:R.75

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

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: K0I.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, H2O.1, H2O.2 MN.14: 4 residues within 4Å: Chain B: H.225, E.227, H.313 Ligands: K0I.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.225, B:E.227, H2O.11, H2O.11

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.47, P.249, H.251, P.293, Y.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.251 GOL.4: 2 residues within 4Å: Chain A: F.63, W.239 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.63 GOL.5: 6 residues within 4Å: Chain A: F.222, C.223, H.225, Q.277, L.278 Ligands: K0I.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.223, A:Q.277 Water bridges: A:Q.277 GOL.6: 2 residues within 4Å: Chain A: M.122, P.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.122 GOL.7: 6 residues within 4Å: Chain A: R.71, F.72, T.73, I.155, D.159, F.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.71, A:T.73, A:T.73, A:T.73, A:D.159 GOL.15: 5 residues within 4Å: Chain B: K.47, P.249, H.251, P.293, Y.295 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.251 GOL.16: 2 residues within 4Å: Chain B: F.63, W.239 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.63 GOL.17: 6 residues within 4Å: Chain B: F.222, C.223, H.225, Q.277, L.278 Ligands: K0I.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.223, B:Q.277 Water bridges: B:Q.277 GOL.18: 2 residues within 4Å: Chain B: M.122, P.123 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.122 GOL.19: 6 residues within 4Å: Chain B: R.71, F.72, T.73, I.155, D.159, F.160 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.71, B:T.73, B:T.73, B:T.73 Water bridges: B:T.73

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 3 residues within 4Å: Chain A: K.52, N.298, C.300 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.54, A:N.298 Water bridges: A:K.52, A:K.52, A:K.52, A:T.129, A:R.296, A:N.298 Salt bridges: A:K.52 SO4.9: 5 residues within 4Å: Chain A: C.65, E.66, V.67, K.68, R.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.65, A:V.67, A:K.68 Salt bridges: A:R.171 SO4.10: 4 residues within 4Å: Chain A: G.95, F.96, Q.98, A.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.95, A:Q.98 Water bridges: A:E.97, A:V.100 SO4.20: 3 residues within 4Å: Chain B: K.52, N.298, C.300 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.54, B:N.298 Water bridges: B:E.20, B:K.52, B:K.52, B:R.296, B:N.298 Salt bridges: B:K.52 SO4.21: 5 residues within 4Å: Chain B: C.65, E.66, V.67, K.68, R.171 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.65, B:V.67, B:K.68 Salt bridges: B:R.171 SO4.22: 4 residues within 4Å: Chain B: G.95, F.96, Q.98, A.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.95, B:Q.98 Water bridges: B:E.97, B:V.100

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

DMS.11: 7 residues within 4Å: Chain A: Q.77, R.78, E.81, C.223, L.278, I.281 Ligands: K0I.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.77 Water bridges: A:R.78 Salt bridges: A:E.81 DMS.12: 6 residues within 4Å: Chain A: M.260, D.273, H.276, Q.277, T.280, Y.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.276 Water bridges: A:D.273 Salt bridges: A:E.257, A:D.273 DMS.23: 7 residues within 4Å: Chain B: Q.77, R.78, E.81, C.223, L.278, I.281 Ligands: K0I.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.77 Water bridges: B:R.78 Salt bridges: B:E.81 DMS.24: 6 residues within 4Å: Chain B: M.260, D.273, H.276, Q.277, T.280, Y.312 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.312 Salt bridges: B:E.257, B:D.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J. Med. Chem. (2018)

Release Date

2018-11-21

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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