SMTL ID : 5k4l.1 (1 other biounit)

Crystal structure of KDM5A in complex with a naphthyridone inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.18 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.473, E.475, S.481, H.561 Ligands: 6QN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.473, A:E.475, A:E.475, A:H.561 NI.5: 5 residues within 4Å: Chain B: H.473, E.475, S.481, H.561 Ligands: 6QN.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.473, B:E.475, B:H.561

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.666, C.669, R.670, T.671, C.689 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.666, A:C.669 ZN.3: 5 residues within 4Å: Chain A: C.680, S.681, C.682, C.697, C.699 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.680, A:C.699 ZN.6: 8 residues within 4Å: Chain B: C.666, A.668, C.669, T.671, V.688, C.689, Y.691, H.692 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.666, B:C.669, B:C.689, B:H.692 ZN.7: 5 residues within 4Å: Chain B: C.680, C.682, C.697, P.698, C.699 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.697, B:C.699

2 x 6QN: ~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide(Non-covalent)

6QN.4: 20 residues within 4Å: Chain A: Y.399, G.400, A.401, Y.462, V.463, G.464, M.465, S.468, S.469, F.470, H.473, E.475, S.481, N.483, K.491, W.493, T.555, H.561, N.565 Ligands: NI.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.399, A:F.470, A:F.470, A:W.493 Hydrogen bonds: A:H.473, A:K.491, A:H.561, A:N.565 pi-Stacking: A:Y.462, A:F.470 6QN.8: 20 residues within 4Å: Chain B: Q.65, Y.399, G.400, A.401, Y.462, V.463, G.464, S.468, S.469, F.470, H.473, E.475, S.481, N.483, K.491, W.493, T.555, H.561, N.565 Ligands: NI.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.399, B:F.470, B:F.470, B:W.493 Hydrogen bonds: B:K.491, B:H.561, B:N.565 pi-Stacking: B:Y.462, B:F.470

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Labadie, S.S. et al., Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-08-10

Peptides

Lysine-specific demethylase 5A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase 5A

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