SMTL ID : 2ozr.1

MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.122, H.126, H.132 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.122, A:H.126, A:H.132, H2O.1, H2O.2 ZN.2: 4 residues within 4Å: Chain A: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.72, A:D.74, A:H.87, A:H.100 ZN.7: 4 residues within 4Å: Chain B: H.122, E.123, H.126, H.132 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.122, B:H.126, B:H.132, H2O.6, H2O.7 ZN.8: 4 residues within 4Å: Chain B: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.72, B:D.74, B:H.87, B:H.100 ZN.13: 4 residues within 4Å: Chain C: H.122, H.126, H.132 Ligands: HAE.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.122, C:H.126, C:H.132 ZN.14: 4 residues within 4Å: Chain C: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.72, C:D.74, C:H.87, C:H.100 ZN.20: 4 residues within 4Å: Chain D: H.122, H.126, H.132 Ligands: HAE.26 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.122, D:H.126, D:H.132, HAE.26 ZN.21: 4 residues within 4Å: Chain D: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.72, D:D.74, D:H.87, D:H.100 ZN.27: 4 residues within 4Å: Chain E: H.122, H.126, H.132 Ligands: HAE.33 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.122, E:H.126, E:H.132 ZN.28: 4 residues within 4Å: Chain E: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.72, E:D.74, E:H.87, E:H.100 ZN.34: 4 residues within 4Å: Chain F: H.122, H.126, H.132 Ligands: HAE.40 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.122, F:H.126, F:H.132, HAE.40 ZN.35: 4 residues within 4Å: Chain F: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.72, F:D.74, F:H.87, F:H.100 ZN.41: 3 residues within 4Å: Chain G: H.122, H.126, H.132 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.122, G:H.126, G:H.132, H2O.33 ZN.42: 4 residues within 4Å: Chain G: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.72, G:D.74, G:H.87, G:H.100 ZN.47: 3 residues within 4Å: Chain H: H.122, H.126, H.132 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.122, H:H.126, H:H.132, H2O.39 ZN.48: 4 residues within 4Å: Chain H: H.72, D.74, H.87, H.100 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.72, H:D.74, H:H.100

24 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.79, G.80, P.81, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.79, A:G.80, A:S.82, A:L.84, A:D.102, A:E.105 CA.4: 5 residues within 4Å: Chain A: D.62, N.94, Y.95, G.96, D.98 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.62, A:N.94, A:G.96, A:D.98, H2O.1, H2O.5 CA.5: 5 residues within 4Å: Chain A: T.26, D.28, D.103, E.105, W.107 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.28, A:D.103, A:D.103, A:E.105, H2O.4 CA.9: 6 residues within 4Å: Chain B: D.79, G.80, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.79, B:G.80, B:S.82, B:L.84, B:D.102, B:E.105 CA.10: 5 residues within 4Å: Chain B: D.62, N.94, Y.95, G.96, D.98 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.62, B:N.94, B:G.96, B:D.98, H2O.6, H2O.9 CA.11: 4 residues within 4Å: Chain B: T.26, D.28, D.103, E.105 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.28, B:D.103, B:D.103, B:E.105, H2O.6 CA.15: 7 residues within 4Å: Chain C: D.79, G.80, P.81, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.79, C:G.80, C:S.82, C:L.84, C:D.102, C:E.105 CA.16: 5 residues within 4Å: Chain C: D.62, N.94, Y.95, G.96, D.98 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.62, C:N.94, C:G.96, C:D.98, H2O.11, H2O.16 CA.17: 4 residues within 4Å: Chain C: T.26, D.28, D.103, E.105 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.28, C:D.103, C:D.103, C:E.105, H2O.16 CA.22: 6 residues within 4Å: Chain D: D.79, G.80, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.79, D:G.80, D:S.82, D:L.84, D:D.102, D:E.105 CA.23: 5 residues within 4Å: Chain D: D.62, N.94, Y.95, G.96, D.98 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.62, D:N.94, D:G.96, D:D.98, H2O.20, H2O.21 CA.24: 5 residues within 4Å: Chain D: T.26, D.28, D.103, E.105, W.107 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.28, D:D.103, D:D.103, D:E.105, H2O.21 CA.29: 6 residues within 4Å: Chain E: D.79, G.80, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain E Metal complexes: E:D.79, E:G.80, E:S.82, E:L.84, E:D.102, E:E.105 CA.30: 5 residues within 4Å: Chain E: A.61, D.62, N.94, G.96, D.98 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.62, E:N.94, E:G.96, E:D.98, H2O.22 CA.31: 5 residues within 4Å: Chain E: T.26, D.28, D.103, E.105, W.107 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.28, E:D.103, E:D.103, E:E.105, H2O.24 CA.36: 6 residues within 4Å: Chain F: D.79, G.80, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain F Metal complexes: F:D.79, F:G.80, F:S.82, F:L.84, F:D.102, F:E.105 CA.37: 5 residues within 4Å: Chain F: A.61, D.62, N.94, G.96, D.98 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.62, F:N.94, F:G.96, F:D.98, H2O.26 CA.38: 4 residues within 4Å: Chain F: T.26, D.28, D.103, E.105 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.28, F:D.103, F:D.103, F:E.105 CA.43: 6 residues within 4Å: Chain G: D.79, G.80, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain G Metal complexes: G:D.79, G:G.80, G:S.82, G:L.84, G:D.102, G:E.105 CA.44: 5 residues within 4Å: Chain G: A.61, D.62, N.94, G.96, D.98 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.62, G:N.94, G:G.96, G:D.98, H2O.34 CA.45: 4 residues within 4Å: Chain G: T.26, D.28, D.103, E.105 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.28, G:D.103, G:D.103, G:E.105 CA.49: 7 residues within 4Å: Chain H: D.79, G.80, P.81, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain H Metal complexes: H:D.79, H:G.80, H:S.82, H:L.84, H:D.102, H:E.105 CA.50: 5 residues within 4Å: Chain H: A.61, D.62, N.94, G.96, D.98 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.62, H:N.94, H:G.96, H:D.98 CA.51: 4 residues within 4Å: Chain H: T.26, D.28, D.103, E.105 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.28, H:D.103, H:D.103, H:E.105, H2O.39

8 x GG1: 4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID(Non-covalent)

GG1.6: 20 residues within 4Å: Chain A: K.40, N.115, F.117, L.118, H.122, A.138, L.139, F.141, P.142, I.143, Y.144, T.145, Y.146, T.147, G.148, K.149, S.150, F.152, M.153, P.155 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.117, A:L.118, A:H.122, A:L.139, A:Y.144, A:Y.146, A:K.149, A:P.155 Hydrogen bonds: A:N.115, A:N.115, A:T.147 Water bridges: A:Y.146, A:M.153 Salt bridges: A:K.40, A:K.149 GG1.12: 20 residues within 4Å: Chain B: K.40, N.115, F.117, L.118, H.122, A.138, L.139, F.141, I.143, Y.144, T.145, Y.146, T.147, G.148, K.149, S.150, H.151, F.152, M.153, P.155 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.117, B:L.118, B:H.122, B:Y.144, B:Y.146, B:K.149, B:F.152, B:P.155 Hydrogen bonds: B:N.115, B:N.115, B:T.147 Salt bridges: B:K.40, B:K.149 GG1.18: 23 residues within 4Å: Chain C: K.40, N.115, F.117, L.118, V.119, H.122, A.138, L.139, F.141, P.142, I.143, Y.144, T.145, Y.146, T.147, G.148, K.149, S.150, H.151, F.152, M.153, P.155 Ligands: HAE.19 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.117, C:L.118, C:H.122, C:Y.144, C:Y.146, C:F.152, C:P.155 Hydrogen bonds: C:N.115, C:T.147 Water bridges: C:M.153 Salt bridges: C:K.40, C:K.149 GG1.25: 22 residues within 4Å: Chain D: K.40, N.115, F.117, L.118, V.119, H.122, A.138, L.139, F.141, P.142, I.143, Y.144, T.145, Y.146, T.147, G.148, K.149, S.150, H.151, F.152, M.153, P.155 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:F.117, D:L.118, D:H.122, D:Y.144, D:Y.146, D:K.149, D:F.152, D:F.152, D:P.155 Hydrogen bonds: D:N.115, D:N.115, D:T.147 Water bridges: D:M.153 Salt bridges: D:K.40, D:K.149 GG1.32: 17 residues within 4Å: Chain E: K.40, N.115, F.117, L.118, V.119, H.122, A.138, L.139, F.141, I.143, Y.144, T.145, Y.146, T.147, F.152, M.153, P.155 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:F.117, E:L.118, E:H.122, E:Y.144, E:Y.146, E:F.152, E:P.155 Hydrogen bonds: E:N.115, E:N.115, E:T.147 Salt bridges: E:K.40 pi-Stacking: E:H.122 GG1.39: 19 residues within 4Å: Chain F: K.40, N.115, F.117, L.118, V.119, H.122, A.138, L.139, F.141, P.142, I.143, Y.144, T.145, Y.146, T.147, K.149, H.151, F.152, M.153 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.118, F:L.118, F:H.122, F:L.139, F:Y.146, F:F.152, F:F.152 Hydrogen bonds: F:N.115, F:N.115, F:T.147, F:T.147 Salt bridges: F:K.40 pi-Stacking: F:H.122 GG1.46: 18 residues within 4Å: Chain G: K.40, N.115, F.117, L.118, V.119, H.122, A.138, L.139, F.141, I.143, Y.144, T.145, Y.146, T.147, K.149, F.152, M.153, P.155 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:F.117, G:L.118, G:H.122, G:L.139, G:Y.144, G:Y.146, G:F.152, G:P.155 Hydrogen bonds: G:N.115, G:N.115, G:T.147, G:K.149 Water bridges: G:K.40 Salt bridges: G:K.40 pi-Stacking: G:H.122, G:Y.144 GG1.52: 19 residues within 4Å: Chain H: K.40, N.115, F.117, L.118, V.119, H.122, A.138, L.139, F.141, P.142, I.143, Y.144, T.145, Y.146, T.147, G.148, F.152, M.153, P.155 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:L.118, H:H.122, H:L.139, H:Y.144, H:Y.146, H:F.152, H:P.155 Hydrogen bonds: H:N.115, H:N.115, H:T.147 Water bridges: H:T.147 Salt bridges: H:K.40

4 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.19: 8 residues within 4Å: Chain C: A.86, H.122, E.123, H.126, H.132, P.142 Ligands: ZN.13, GG1.18 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.86 HAE.26: 7 residues within 4Å: Chain D: A.86, H.122, E.123, H.126, H.132, P.142 Ligands: ZN.20 No protein-ligand interaction detected (PLIP) HAE.33: 6 residues within 4Å: Chain E: H.122, E.123, H.126, H.132, P.142 Ligands: ZN.27 No protein-ligand interaction detected (PLIP) HAE.40: 5 residues within 4Å: Chain F: A.86, H.122, H.126, H.132 Ligands: ZN.34 1 PLIP interactions: 1 interactions with chain F Water bridges: F:A.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, A.R. et al., Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects. J.Biol.Chem. (2007)

Release Date

2007-07-24

Peptides

Collagenase 3: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Collagenase 3

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