SMTL ID : 4nbl.1

Tailoring Small Molecules for an Allosteric Site on Procaspase-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

1 x 2J6: 5-fluoro-2-({[3-(pyrimidin-2-yl)pyridin-2-yl]amino}methyl)phenol(Non-covalent)

2J6.1: 11 residues within 4Å: Chain A: Y.178, T.179, L.180, P.181 Chain B: A.175, S.176, V.177, Y.178, T.179, L.180, E.194 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.178, B:Y.178, B:L.180, B:E.194, A:Y.178 Hydrogen bonds: B:T.179 pi-Stacking: B:Y.178, B:Y.178, A:Y.178 Water bridges: A:Q.117, A:Q.117, A:Q.117

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

PO4.2: 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:S.100, A:Q.141, A:A.143, A:S.198, A:S.198 Water bridges: A:R.44, A:R.44, A:D.173, A:D.173 Salt bridges: A:R.44, A:H.101, A:R.200 PO4.3: 8 residues within 4Å: Chain A: K.124, G.125, K.136, G.183, A.184, F.186 Chain B: Y.196, K.253 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.125, A:A.184, A:A.184 Salt bridges: A:K.136, B:K.253 PO4.4: 8 residues within 4Å: Chain A: Y.196, K.253 Chain B: K.124, G.125, K.136, G.183, A.184, F.186 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.125, B:A.184, B:A.184, B:A.184, A:Y.196 Water bridges: B:K.136 Salt bridges: B:K.136, A:K.253 PO4.5: 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:S.100, B:Q.141, B:A.143, B:S.198, B:S.198 Water bridges: B:R.44, B:R.44, B:D.173, B:D.173 Salt bridges: B:R.44, B:H.101, B:R.200 PO4.6: 1 residues within 4Å: Chain B: N.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.69 PO4.7: 2 residues within 4Å: Chain B: R.144, A.174 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.146, B:N.146, B:A.174, B:A.174 Salt bridges: B:R.144

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

2014-01-01

Peptides

Caspase-6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Caspase-6

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