SMTL ID : 3ked.1

Crystal structure of Aminopeptidase N in complex with 2,4-diaminobutyric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.318, H.322, E.341, Y.402 Ligands: DAB.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.318, A:H.322, A:E.341, A:E.341

1 x DAB: 2,4-DIAMINOBUTYRIC ACID(Non-covalent)

DAB.2: 13 residues within 4Å: Chain A: E.142, M.281, A.283, M.284, E.285, H.318, E.319, H.322, K.340, E.341, Y.402 Ligands: ZN.1, MLA.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.142, A:M.281, A:A.283, A:K.340, A:Y.402 Salt bridges: A:H.318, A:H.322

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: S.353, D.354, G.356, R.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.354, A:R.358 NA.4: 1 residues within 4Å: Chain A: D.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.473, A:D.473, A:D.473

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: A.552, L.553, W.567, L.575, D.587, A.588, S.591 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.553, A:D.587, A:D.587, A:S.591, A:S.591 Water bridges: A:S.591 GOL.6: 7 residues within 4Å: Chain A: S.84, V.85, P.91, W.92, T.93, W.95 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.85, A:V.85, A:W.95 GOL.7: 5 residues within 4Å: Chain A: L.82, V.83, S.84, W.95 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.8: 7 residues within 4Å: Chain A: Y.397, T.398, L.399, Y.402, E.403, R.846 Ligands: MLA.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.398, A:R.846 GOL.9: 6 residues within 4Å: Chain A: R.702, Q.724, A.728, N.729, N.730, D.733 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.702, A:R.702, A:N.729, A:N.729, A:D.733 Water bridges: A:N.729 GOL.10: 2 residues within 4Å: Chain A: V.691, E.692 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.691 GOL.11: 1 residues within 4Å: Chain A: H.32 No protein-ligand interaction detected (PLIP) GOL.12: 6 residues within 4Å: Chain A: K.29, E.144, D.333, W.334, F.335, M.393 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.144, A:W.334 Water bridges: A:E.144, A:R.147, A:I.391 GOL.13: 3 residues within 4Å: Chain A: L.610, S.611, L.612 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.611, A:L.612, A:L.612

3 x MLA: MALONIC ACID(Non-covalent)

MLA.14: 6 residues within 4Å: Chain A: R.662, E.663, T.666, R.707, F.711, A.743 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.711 Water bridges: A:R.662, A:E.663, A:E.663, A:T.666 Salt bridges: A:R.662, A:R.662, A:R.707 MLA.15: 7 residues within 4Å: Chain A: R.314, V.315, H.318, D.348, Y.402 Ligands: DAB.2, GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.315 Hydrogen bonds: A:A.283 Salt bridges: A:R.314, A:H.318, A:H.318 MLA.16: 4 residues within 4Å: Chain A: E.90, P.91, W.92, T.93 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.90 Hydrogen bonds: A:E.90, A:P.91, A:T.93, A:T.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gumpena, R. et al., Discovery of alpha, beta- and alpha, gamma-Diamino Acid Scaffolds for the Inhibition of M1 Family Aminopeptidases. Chemmedchem (2011)

Release Date

2010-11-03

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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