SMTL ID : 3pvk.1

Secreted aspartic protease 2 in complex with benzamidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.57 Ligands: IMD.5, IMD.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.57, A:D.57

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 10 residues within 4Å: Chain A: Y.84, G.85, D.86, G.220, T.221, Y.225, N.301, I.305 Ligands: BEN.3, MPD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.221, A:Y.225, A:I.305 Hydrogen bonds: A:D.86, A:T.221 BEN.3: 9 residues within 4Å: Chain A: D.32, G.34, S.35, Y.84, L.216, D.218, I.305 Ligands: BEN.2, MPD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.216, A:I.305 Hydrogen bonds: A:D.32, A:G.34, A:D.218

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 9 residues within 4Å: Chain A: I.30, D.32, Y.84, S.88, I.119, I.123, G.220 Ligands: BEN.2, BEN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.30, A:Y.84, A:Y.84, A:I.119, A:I.119, A:I.123

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 3 residues within 4Å: Chain A: D.57 Ligands: ZN.1, IMD.6 No protein-ligand interaction detected (PLIP) IMD.6: 5 residues within 4Å: Chain A: T.55, D.57, Q.61 Ligands: ZN.1, IMD.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Behnen, J. et al., Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Chemmedchem (2012)

Release Date

2011-12-07

Peptides

Candidapepsin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Candidapepsin-2

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