SMTL ID : 7rnd.1

Crystal structure of caspase-3 with inhibitor Ac-VDPVD-CHO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

2 x VAL- ASP- PRO- VAL- ASA: Ac-VDPVD-CHO(Non-covalent)

VAL-ASP-PRO-VAL-ASA.1: 16 residues within 4Å: Chain A: R.31, S.87, H.88, G.89, Q.128, C.130 Chain B: Y.21, S.22, W.23, R.24, N.25, S.26, W.31, E.65, S.66, F.67 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.21, B:Y.21, B:W.23, B:F.67 Hydrogen bonds: B:S.22, B:R.24, B:R.24, B:R.24, B:R.24, B:N.25, B:F.67, A:G.89, A:Q.128, A:C.130 Salt bridges: B:R.24, A:R.31, A:H.88 VAL-ASP-PRO-VAL-ASA.2: 16 residues within 4Å: Chain C: R.31, S.87, H.88, G.89, Q.128, C.130 Chain D: Y.21, S.22, W.23, R.24, N.25, S.26, W.31, E.65, S.66, F.67 20 PLIP interactions: 14 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:Y.21, D:Y.21, D:W.23 Hydrogen bonds: D:S.22, D:R.24, D:R.24, D:R.24, D:R.24, D:R.24, D:N.25, D:S.26, D:S.26, D:F.67, C:H.88, C:G.89, C:Q.128, C:C.130 Salt bridges: D:R.24, C:R.31, C:H.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bresinsky, M. et al., Structure-Based Design and Biological Evaluation of Novel Caspase-2 Inhibitors Based on the Peptide AcVDVAD-CHO and the Caspase-2-Mediated Tau Cleavage Sequence YKPVD314. Acs Pharmacol Transl Sci (2022)

Release Date

2022-01-05

Peptides

Caspase-3 subunit p17: AC
Caspase-3 subunit p12: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Caspase-3 subunit p17

Caspase-3 subunit p12

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