SMTL ID : 4a7b.1

MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR CMPD22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x 3W5: N-[(3S)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide(Non-covalent)

3W5.1: 18 residues within 4Å: Chain A: G.80, L.81, L.82, A.83, L.115, V.116, H.119, E.120, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149 Ligands: HAE.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.82, A:V.116, A:H.119, A:Y.141, A:Y.141 Hydrogen bonds: A:L.82, A:A.83, A:P.139, A:T.142, A:T.142, A:T.144 3W5.17: 18 residues within 4Å: Chain C: G.80, L.81, L.82, A.83, L.115, V.116, H.119, E.120, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149 Ligands: HAE.18 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.82, C:V.116, C:H.119, C:Y.141, C:Y.141 Hydrogen bonds: C:L.82, C:A.83, C:P.139, C:T.142 Water bridges: C:T.142

4 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.2: 9 residues within 4Å: Chain A: L.81, A.83, H.84, H.119, E.120, H.123, H.129 Ligands: 3W5.1, ZN.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.81, A:H.84 Hydrogen bonds: A:A.83 HAE.10: 8 residues within 4Å: Chain B: L.81, A.83, H.84, H.119, E.120, H.123 Ligands: 3W4.9, ZN.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.81 Hydrogen bonds: B:E.120 HAE.18: 9 residues within 4Å: Chain C: L.81, A.83, H.84, H.119, E.120, H.123, H.129 Ligands: 3W5.17, ZN.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.81, C:H.84 Hydrogen bonds: C:A.83 HAE.26: 8 residues within 4Å: Chain D: L.81, A.83, H.84, H.119, E.120, H.123 Ligands: 3W4.25, ZN.28 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.81 Hydrogen bonds: D:E.120

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.34, K.37, S.106, N.112, F.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.37, A:K.37, A:N.112 Water bridges: A:T.105, A:N.112 GOL.11: 3 residues within 4Å: Chain B: A.85, F.86, P.87 No protein-ligand interaction detected (PLIP) GOL.19: 5 residues within 4Å: Chain C: A.34, K.37, S.106, N.112, F.114 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.37, C:K.37, C:N.112 Water bridges: C:T.105, C:N.112 GOL.27: 3 residues within 4Å: Chain D: A.85, F.86, P.87 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: HAE.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.119, A:H.123, A:H.129, HAE.2 ZN.6: 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.12: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: HAE.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.119, B:H.123, B:H.129, HAE.10 ZN.13: 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.20: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: HAE.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.119, C:H.123, C:H.129, HAE.18 ZN.22: 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.28: 4 residues within 4Å: Chain D: H.119, H.123, H.129 Ligands: HAE.26 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.119, D:H.123, D:H.129, HAE.26 ZN.29: 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

8 x CA: CALCIUM ION(Non-covalent)

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.2, H2O.2 CA.7: 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.14: 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.7, H2O.7 CA.15: 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.21: 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.10, H2O.10 CA.23: 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.30: 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.15, H2O.15 CA.31: 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 NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.25 NA.16: 4 residues within 4Å: Chain B: T.23, D.25, D.100, E.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.25 NA.24: 4 residues within 4Å: Chain C: T.23, D.25, D.100, E.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.23, C:D.100, C:D.100 NA.32: 4 residues within 4Å: Chain D: T.23, D.25, D.100, E.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.23, D:D.100, D:D.100

2 x 3W4: N-[(3R)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide(Non-covalent)

3W4.9: 17 residues within 4Å: Chain B: G.80, L.81, L.82, L.115, V.116, H.119, E.120, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149 Ligands: HAE.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.81, B:L.82, B:V.116, B:H.119, B:Y.141, B:F.149 Hydrogen bonds: B:A.83, B:P.139, B:T.142, B:T.142 3W4.25: 17 residues within 4Å: Chain D: G.80, L.81, L.82, L.115, V.116, H.119, E.120, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149 Ligands: HAE.26 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.81, D:L.82, D:V.116, D:H.119, D:Y.141, D:F.149 Hydrogen bonds: D:L.82, D:A.83, D:P.139, D:T.142 Water bridges: D:T.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Savi, C. et al., Lead Optimisation of Selective Non-Zinc Binding Inhibitors of Mmp13. Part 2. Bioorg.Med.Chem.Lett. (2012)

Release Date

2011-12-21

Peptides

COLLAGENASE 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

COLLAGENASE 3

Related Entries With Identical Sequence