SMTL ID : 5v9p.1

Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone (compound 35) in complex with KDM5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: 90S.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: 4 residues within 4Å: Chain A: C.666, C.669, 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.682, A:C.699

1 x 90S: [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone(Non-covalent)

90S.4: 16 residues within 4Å: Chain A: A.401, W.460, Y.462, F.470, H.473, E.475, S.481, N.483, K.491, W.493, H.561, N.565, A.573, V.574, N.575 Ligands: NI.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.460, A:F.470, A:W.493 Hydrogen bonds: A:K.491, A:N.575 pi-Stacking: A:F.470

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

SO4.5: 6 residues within 4Å: Chain A: R.63, A.401, D.402, I.403, W.460, Y.462 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.402, A:Y.462, A:Y.462

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
A

B
B

Lysine-specific demethylase 5A

Lysine-specific demethylase 5A

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