SMTL ID : 3i7g.2 (1 other biounit)

MMP-13 in complex with a non zinc-chelating inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: FMT.6 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: FMT.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 ZN.14: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: FMT.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.123, C:H.129 ZN.15: 4 residues within 4Å: Chain C: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.69, C:D.71, C:H.84, C:H.97 ZN.21: 4 residues within 4Å: Chain D: H.119, H.123, H.129 Ligands: FMT.26 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.123, D:H.129 ZN.22: 4 residues within 4Å: Chain D: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.69, D:D.71, D:H.84, D:H.97

12 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102 CA.4: 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.5: 6 residues within 4Å: Chain A: A.58, D.59, N.91, Y.92, G.93, D.95 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:G.93, A:D.95, H2O.47, H2O.89 CA.10: 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.424 CA.11: 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.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.245, H2O.262 CA.16: 4 residues within 4Å: Chain C: T.23, D.25, D.100, E.102 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.25, C:D.100, C:D.100, C:E.102 CA.17: 7 residues within 4Å: Chain C: D.76, G.77, P.78, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.76, C:G.77, C:S.79, C:L.81, C:D.99, C:E.102 CA.18: 6 residues within 4Å: Chain C: A.58, D.59, N.91, Y.92, G.93, D.95 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.59, C:G.93, C:D.95, H2O.393, H2O.435 CA.23: 4 residues within 4Å: Chain D: T.23, D.25, D.100, E.102 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.25, D:D.100, D:D.100, D:E.102, H2O.78 CA.24: 6 residues within 4Å: Chain D: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.76, D:G.77, D:S.79, D:L.81, D:D.99, D:E.102 CA.25: 5 residues within 4Å: Chain D: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.59, D:N.91, D:G.93, D:D.95, H2O.591, H2O.608

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 7 residues within 4Å: Chain A: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.1, 732.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.85 FMT.13: 6 residues within 4Å: Chain B: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.120 FMT.19: 7 residues within 4Å: Chain C: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.14, 732.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.120 Water bridges: C:A.85 FMT.26: 6 residues within 4Å: Chain D: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.120

2 x 732: 5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE(Non-covalent)

732.7: 15 residues within 4Å: Chain A: G.80, L.81, L.82, A.83, Y.111, L.115, V.116, H.119, E.120, L.136, F.138, P.139, I.140, Y.141 Ligands: FMT.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.116, A:H.119, A:Y.141 Hydrogen bonds: A:G.80, A:L.82, A:A.83, A:P.139, A:Y.141 pi-Stacking: A:H.119 732.20: 15 residues within 4Å: Chain C: G.80, L.81, L.82, A.83, Y.111, L.115, V.116, H.119, E.120, L.136, F.138, P.139, I.140, Y.141 Ligands: FMT.19 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.116, C:H.119, C:Y.141 Hydrogen bonds: C:G.80, C:L.82, C:A.83, C:P.139, C:Y.141 pi-Stacking: C:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heim-Riether, A. et al., Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors. Bioorg.Med.Chem.Lett. (2009)

Release Date

2009-09-01

Peptides

Collagenase 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Collagenase 3

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