SMTL ID : 3zxh.1 (1 other biounit)

MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 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: E41.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.119, A:H.123, A:H.129, E41.7 ZN.2: 6 residues within 4Å: Chain A: H.69, D.71, Y.73, H.84, F.86, 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.9: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: E41.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.119, B:H.123, B:H.129, E41.14 ZN.10: 5 residues within 4Å: Chain B: H.69, D.71, Y.73, 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.19: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: E41.25 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.119, C:H.123, C:H.129, E41.25 ZN.20: 6 residues within 4Å: Chain C: H.69, D.71, Y.73, H.84, F.86, 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.27: 4 residues within 4Å: Chain D: H.119, H.123, H.129 Ligands: E41.32 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.123, D:H.129 ZN.28: 5 residues within 4Å: Chain D: H.69, D.71, Y.73, 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

14 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: 7 residues within 4Å: Chain A: T.23, P.24, D.25, D.100, E.102, T.103, 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.2 CA.5: 8 residues within 4Å: Chain A: W.10, D.59, I.60, M.61, 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.4, H2O.5 CA.6: 6 residues within 4Å: Chain A: S.43, D.44, T.46, P.47, G.166, D.167 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.43, A:T.46, H2O.3, H2O.3, H2O.3, H2O.3 CA.11: 7 residues within 4Å: Chain B: D.76, G.77, P.78, 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: 7 residues within 4Å: Chain B: T.23, P.24, D.25, D.100, E.102, T.103, W.104 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.10 CA.13: 7 residues within 4Å: Chain B: D.59, I.60, M.61, 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.12, H2O.12 CA.21: 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.22: 7 residues within 4Å: Chain C: T.23, P.24, D.25, D.100, E.102, T.103, W.104 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.25, C:D.100, C:D.100, C:E.102, H2O.18 CA.23: 8 residues within 4Å: Chain C: W.10, D.59, I.60, M.61, 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.20, H2O.20 CA.24: 6 residues within 4Å: Chain C: S.43, D.44, T.46, P.47, G.166, D.167 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.43, C:T.46, H2O.19, H2O.19, H2O.19, H2O.19 CA.29: 7 residues within 4Å: Chain D: D.76, G.77, P.78, 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.30: 7 residues within 4Å: Chain D: T.23, P.24, D.25, D.100, E.102, T.103, W.104 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.26 CA.31: 7 residues within 4Å: Chain D: D.59, I.60, M.61, 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.28, H2O.28

4 x E41: N-hydroxy-N^2^-(3-methylbutyl)-N^2^-(naphthalen-2-ylsulfonyl)-D-valinamide(Non-covalent)

E41.7: 15 residues within 4Å: Chain A: L.81, L.82, A.83, H.84, V.116, H.119, E.120, H.123, H.129, F.138, P.139, I.140, Y.141 Ligands: ZN.1, GOL.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.81, A:L.82, A:H.119, A:P.139, A:Y.141 Hydrogen bonds: A:L.82, A:A.83 pi-Stacking: A:H.119 E41.14: 17 residues within 4Å: Chain B: G.80, L.81, L.82, A.83, H.84, V.116, H.119, E.120, H.123, H.129, F.138, P.139, I.140, Y.141 Ligands: ZN.9, GOL.17, GOL.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.81, B:L.82, B:V.116, B:H.119, B:P.139 Hydrogen bonds: B:L.82, B:A.83 pi-Stacking: B:H.119 E41.25: 15 residues within 4Å: Chain C: L.81, L.82, A.83, H.84, V.116, H.119, E.120, H.123, H.129, F.138, P.139, I.140, Y.141 Ligands: ZN.19, GOL.26 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.81, C:L.82, C:H.119, C:P.139, C:Y.141 Hydrogen bonds: C:L.82, C:A.83 pi-Stacking: C:H.119 E41.32: 17 residues within 4Å: Chain D: G.80, L.81, L.82, A.83, H.84, V.116, H.119, E.120, H.123, H.129, F.138, P.139, I.140, Y.141 Ligands: ZN.27, GOL.35, GOL.36 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.81, D:L.82, D:V.116, D:H.119, D:P.139 Hydrogen bonds: D:L.82, D:A.83, D:A.83, D:E.120 pi-Stacking: D:H.119

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: L.115, A.135, L.136, I.140, Y.141, T.142, Y.143, T.144, F.149 Ligands: E41.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.142, A:T.142, A:T.144 Water bridges: A:A.135 GOL.15: 7 residues within 4Å: Chain B: P.78, S.79, D.101, E.102, T.103, G.110, Y.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.102, B:T.103, B:T.103, B:T.103, B:T.103 GOL.16: 10 residues within 4Å: Chain B: G.65, I.66, K.67, E.68, H.69 Chain C: V.20, S.63, H.69, G.70, H.97 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Water bridges: C:N.21, C:N.21, C:N.21, C:G.70, C:H.97, C:H.97 Hydrogen bonds: B:I.66, B:I.66 GOL.17: 10 residues within 4Å: Chain B: L.115, A.135, L.136, I.140, Y.141, T.142, Y.143, T.144, F.149 Ligands: E41.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.142, B:T.142 Water bridges: B:A.135, B:F.138, B:T.142 GOL.18: 7 residues within 4Å: Chain B: S.79, G.80, L.82, Y.111, I.140, Y.141 Ligands: E41.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.80, B:G.80, B:Y.111, B:Y.141 Water bridges: B:Y.111 GOL.26: 10 residues within 4Å: Chain C: L.115, A.135, L.136, I.140, Y.141, T.142, Y.143, T.144, F.149 Ligands: E41.25 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.142, C:T.142, C:T.144 Water bridges: C:A.135 GOL.33: 7 residues within 4Å: Chain D: P.78, S.79, D.101, E.102, T.103, G.110, Y.111 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.103, D:T.103, D:T.103, D:T.103 GOL.34: 10 residues within 4Å: Chain A: V.20, S.63, H.69, G.70, H.97 Chain D: G.65, I.66, K.67, E.68, H.69 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Water bridges: A:N.21, A:N.21, A:N.21, A:D.71, A:H.97, A:H.97 Hydrogen bonds: D:I.66, D:I.66 GOL.35: 10 residues within 4Å: Chain D: L.115, A.135, L.136, I.140, Y.141, T.142, Y.143, T.144, F.149 Ligands: E41.32 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.142, D:T.142 Water bridges: D:A.135, D:F.138, D:T.142 GOL.36: 7 residues within 4Å: Chain D: S.79, G.80, L.82, Y.111, I.140, Y.141 Ligands: E41.32 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.80, D:G.80, D:Y.111, D:Y.141 Water bridges: D:Y.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tommasi, R.A. et al., Potent and Selective 2-Naphthylsulfonamide Substituted Hydroxamic Acid Inhibitors of Matrix Metalloproteinase-13. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-10-19

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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