SMTL ID : 5v9t.2 (1 other biounit)

Crystal structure of selective pyrrolidine amide KDM5a inhibitor N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide (compound 48)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-1-1-mer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.473, E.475, S.481, H.561 Ligands: 90V.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.473, A:E.475, A:H.561

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.666, A.668, C.669, T.671, C.689, H.692 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.666, A:C.669, A:C.689 ZN.3: 5 residues within 4Å: Chain A: C.680, S.681, C.682, C.697, C.699 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.680, A:C.682, A:C.699

1 x 90V: N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide(Non-covalent)

90V.4: 22 residues within 4Å: Chain A: Y.399, G.400, A.401, W.460, Y.462, G.464, S.468, S.469, F.470, H.473, E.475, S.481, N.483, K.491, W.493, H.561, N.565, A.571, A.573, V.574, N.575 Ligands: NI.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.462, A:Y.462, A:F.470, A:A.573 Hydrogen bonds: A:S.481, A:K.491, A:N.565, A:N.575

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, J. et al., From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-05-10

Peptides

Lysine-specific demethylase 5A: A
Lysine-specific demethylase 5A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

Lysine-specific demethylase 5A

Lysine-specific demethylase 5A

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