SMTL ID : 3elm.2 (1 other biounit)

Crystal Structure of MMP-13 Complexed with Inhibitor 24f

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: 24F.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97 ZN.8: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: 24F.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.123, B:H.129 ZN.9: 4 residues within 4Å: Chain B: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.69, B:D.71, B:H.84, B:H.97

7 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.76, G.77, P.78, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102 CA.4: 5 residues within 4Å: Chain A: T.23, D.25, D.100, E.102, W.104 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102, H2O.4 CA.5: 5 residues within 4Å: Chain A: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.3, H2O.4 CA.6: 2 residues within 4Å: Chain A: S.43, T.46 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.43, A:T.46, H2O.1, H2O.1, H2O.1, H2O.4 CA.10: 6 residues within 4Å: Chain B: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.76, B:G.77, B:S.79, B:L.81, B:D.99, B:E.102 CA.11: 4 residues within 4Å: Chain B: T.23, D.25, D.100, E.102 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.25, B:D.100, B:D.100, B:E.102, H2O.8 CA.12: 5 residues within 4Å: Chain B: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:N.91, B:G.93, B:D.95, H2O.9, H2O.9

2 x 24F: (2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1-[(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid(Non-covalent)

24F.7: 21 residues within 4Å: Chain A: Y.73, L.81, L.82, A.83, H.84, A.85, F.86, L.115, V.116, H.119, E.120, H.123, H.129, A.135, L.136, F.138, P.139, I.140, Y.141, T.142 Ligands: ZN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.73, A:L.81, A:L.82, A:F.86, A:L.115, A:V.116, A:H.119, A:Y.141 Hydrogen bonds: A:L.82, A:A.83, A:A.83 Salt bridges: A:H.119, A:H.123, A:H.129 pi-Stacking: A:H.119 24F.13: 19 residues within 4Å: Chain B: Y.73, L.81, L.82, A.83, H.84, F.86, L.115, V.116, H.119, E.120, H.123, H.129, A.135, L.136, F.138, P.139, I.140, Y.141 Ligands: ZN.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.73, B:L.81, B:L.82, B:F.86, B:V.116, B:H.119, B:Y.141 Hydrogen bonds: B:L.82, B:A.83, B:A.83 Salt bridges: B:H.119, B:H.123, B:H.129 pi-Stacking: B:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monovich, L.G. et al., Discovery of potent, selective, and orally active carboxylic acid based inhibitors of matrix metalloproteinase-13. J.Med.Chem. (2009)

Release Date

2009-07-21

Peptides

Collagenase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Collagenase 3

Related Entries With Identical Sequence