SMTL ID : 4nbn.1

Tailoring Small Molecules for an Allosteric Site on Procaspase-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: S.87, C.128, H.129, S.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.130 Water bridges: A:H.129, A:H.129 PO4.2: 4 residues within 4Å: Chain A: E.201, N.204, Q.210, R.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.204, A:Q.210, A:Q.210 Salt bridges: A:R.239 PO4.3: 2 residues within 4Å: Chain A: H.21, K.134 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.18, A:G.133, A:G.133 Salt bridges: A:H.21, A:K.134 PO4.4: 9 residues within 4Å: Chain A: R.44, S.100, H.101, Q.141, A.142, A.143, D.173, S.198, R.200 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.141, A:A.143, A:D.173, A:D.173, A:D.173, A:S.198 Water bridges: A:R.44, A:R.44, A:D.173 Salt bridges: A:R.44, A:H.101, A:R.200 PO4.5: 8 residues within 4Å: Chain A: K.124, G.125, K.136, G.183, A.184, F.186 Chain B: Y.196, K.253 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.196, B:Y.196, A:G.125, A:A.184 Salt bridges: B:K.253, A:K.136 Water bridges: A:K.136 PO4.7: 2 residues within 4Å: Chain B: R.144, A.174 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.174, B:A.174 Salt bridges: B:R.144 PO4.8: 9 residues within 4Å: Chain B: R.44, S.100, H.101, Q.141, A.142, A.143, D.173, S.198, R.200 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.141, B:A.143, B:D.173, B:D.173, B:D.173, B:S.198 Water bridges: B:R.44, B:R.44, B:D.173 Salt bridges: B:R.44, B:H.101, B:R.200 PO4.9: 2 residues within 4Å: Chain B: H.21, K.134 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.18, B:H.21, B:K.134 Salt bridges: B:H.21, B:K.134 PO4.10: 8 residues within 4Å: Chain A: Y.196, K.253 Chain B: K.124, G.125, K.136, G.183, A.184, F.186 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.196, B:G.125, B:A.184 Salt bridges: A:K.253, B:K.136 Water bridges: B:K.136

1 x 2J7: 2,2'-[pyrimidine-4,6-diylbis(iminomethanediyl)]diphenol(Non-covalent)

2J7.6: 12 residues within 4Å: Chain A: V.177, Y.178, T.179, L.180, P.181, E.194 Chain B: V.177, Y.178, T.179, L.180, P.181, E.194 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:E.194, A:E.194, B:Y.178, B:E.194, B:E.194 Hydrogen bonds: A:T.179, B:T.179, B:T.179 pi-Stacking: A:Y.178, B:Y.178 Water bridges: B:Y.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, J. et al., Tailoring small molecules for an allosteric site on procaspase-6. Chemmedchem (2014)

Release Date

2013-12-18

Peptides

Caspase-6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Caspase-6

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