SMTL ID : 3kry.5 (4 other biounits)

Crystal structure of MMP-13 in complex with SC-78080

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: 3KR.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.6: 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.7: 5 residues within 4Å: Chain B: H.119, E.120, H.123, H.129 Ligands: 3KR.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.123, B:H.129 ZN.11: 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.12: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: 3KR.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.123, C:H.129 ZN.16: 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 ZN.17: 4 residues within 4Å: Chain D: H.119, H.123, H.129 Ligands: 3KR.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.123, D:H.129

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.1, H2O.4 CA.4: 6 residues within 4Å: Chain A: D.76, G.77, 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.8: 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.5, H2O.8 CA.9: 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.13: 5 residues within 4Å: Chain C: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.59, C:N.91, C:G.93, C:D.95, H2O.11, H2O.12 CA.14: 6 residues within 4Å: Chain C: D.76, G.77, 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: 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.16, H2O.17 CA.19: 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

4 x 3KR: 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide(Non-covalent)

3KR.5: 19 residues within 4Å: Chain A: G.80, L.81, L.82, A.83, 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, T.144 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.81, A:L.115, A:V.116, A:P.139, A:Y.141 Hydrogen bonds: A:T.142 Halogen bonds: A:A.135 3KR.10: 19 residues within 4Å: Chain B: G.80, L.81, L.82, A.83, 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, T.144 Ligands: ZN.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.81, B:L.115, B:V.116, B:P.139, B:Y.141 Hydrogen bonds: B:T.142 Halogen bonds: B:A.135 3KR.15: 19 residues within 4Å: Chain C: G.80, L.81, L.82, A.83, 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, T.144 Ligands: ZN.12 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.81, C:V.116, C:H.119, C:P.139, C:Y.141 Hydrogen bonds: C:T.142 Halogen bonds: C:A.135 3KR.20: 19 residues within 4Å: Chain D: G.80, L.81, L.82, A.83, 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, T.144 Ligands: ZN.17 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.81, D:L.115, D:V.116, D:P.139, D:Y.141 Hydrogen bonds: D:T.142 Halogen bonds: D:A.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Becker, D.P. et al., Orally-active MMP-1 sparing alpha-tetrahydropyranyl and alpha-piperidinyl sulfone matrix metalloproteinase (MMP) inhibitors with efficacy in cancer, arthritis, and cardiovascular disease. J.Med.Chem. (2010)

Release Date

2010-10-06

Peptides

Collagenase 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

Collagenase 3

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