SMTL ID : 5fjk.1

Crystal structure of human JMJD2C catalytic domain in complex 6-ethyl- 5-methyl-7-oxo-4,7-dihydropyrazolo(1,5-a)pyrimidine-3-carbonitrile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.238, H.244, C.310, T.311, C.312 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

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

NI.2: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: EM6.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.9, H2O.9

1 x EM6: 6-ethyl-5-methyl-7-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

EM6.3: 11 residues within 4Å: Chain A: Y.136, Y.181, T.188, F.189, H.192, N.202, K.210, W.212, H.280, N.284 Ligands: NI.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.136, A:Y.136, A:Y.181 Hydrogen bonds: A:N.202, A:K.210, A:N.284 Water bridges: A:G.183 pi-Stacking: A:F.189

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: N.128, W.185 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: Y.181, S.292 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: D.239, A.240, F.241, L.242 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: P.113, R.114 Ligand excluded by PLIP

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

EDO.8: 4 residues within 4Å: Chain A: N.90, I.91, Q.92 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.90 EDO.9: 4 residues within 4Å: Chain A: I.91, Q.92, K.93 Ligands: EDO.8 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: E.56, W.57, K.58, E.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.56, A:K.58, A:E.151 Water bridges: A:Q.61, A:D.150 EDO.11: 6 residues within 4Å: Chain A: Y.118, E.119, E.122, S.211, K.263, T.265 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain A: Q.329, P.330, D.331, R.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.331, A:D.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cecatiello, V. et al., Crystal Structures of Human Jmjd2C Catalytic Domain Bound to Inhibitors. To be Published

Release Date

2015-10-21

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4C

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