SMTL ID : 1utt.1

Crystal Structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl-4-(4-ethoxy[1,1-biphenyl]-4-yl)-4-oxobutanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.1: 8 residues within 4Å: Chain A: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: CP8.2, ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.77 HAE.9: 8 residues within 4Å: Chain B: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: CP8.10, ZN.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.77 HAE.17: 8 residues within 4Å: Chain C: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: CP8.18, ZN.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.77 HAE.25: 8 residues within 4Å: Chain D: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: CP8.26, ZN.27 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.77 HAE.33: 8 residues within 4Å: Chain E: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: CP8.34, ZN.35 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.77 HAE.41: 8 residues within 4Å: Chain F: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: CP8.42, ZN.43 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.77

6 x CP8: 2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL) ETHYL-4-(4'-ETHOXY [1,1'-BIPHENYL]-4-YL)-4-OXOBUTANOIC ACID(Non-covalent)

CP8.2: 18 residues within 4Å: Chain A: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136 Chain D: G.74 Ligands: HAE.1, CP8.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.113, A:Y.135 Hydrogen bonds: A:L.76, A:A.77, A:K.136 CP8.10: 18 residues within 4Å: Chain B: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136 Chain E: G.74 Ligands: HAE.9, CP8.34 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.113, B:Y.135 Hydrogen bonds: B:L.76, B:A.77, B:K.136 CP8.18: 18 residues within 4Å: Chain C: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136 Chain F: G.74 Ligands: HAE.17, CP8.42 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:H.113, C:Y.135 Hydrogen bonds: C:L.76, C:A.77, C:E.114, C:K.136 CP8.26: 18 residues within 4Å: Chain A: G.74 Chain D: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136 Ligands: CP8.2, HAE.25 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:H.113, D:Y.135 Hydrogen bonds: D:L.76, D:A.77, D:E.114, D:K.136 CP8.34: 18 residues within 4Å: Chain B: G.74 Chain E: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136 Ligands: CP8.10, HAE.33 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:H.113, E:Y.135 Hydrogen bonds: E:L.76, E:A.77, E:K.136 CP8.42: 18 residues within 4Å: Chain C: G.74 Chain F: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136 Ligands: CP8.18, HAE.41 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:H.113, F:Y.135 Hydrogen bonds: F:L.76, F:A.77, F:E.114, F:K.136

12 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.113, H.117, H.123 Ligands: HAE.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.113, A:H.117, A:H.123, HAE.1 ZN.4: 4 residues within 4Å: Chain A: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.63, A:D.65, A:H.78, A:H.91 ZN.11: 4 residues within 4Å: Chain B: H.113, H.117, H.123 Ligands: HAE.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.113, B:H.117, B:H.123, HAE.9 ZN.12: 4 residues within 4Å: Chain B: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.63, B:D.65, B:H.78, B:H.91 ZN.19: 4 residues within 4Å: Chain C: H.113, H.117, H.123 Ligands: HAE.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.113, C:H.117, C:H.123, HAE.17 ZN.20: 4 residues within 4Å: Chain C: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.63, C:D.65, C:H.78, C:H.91 ZN.27: 4 residues within 4Å: Chain D: H.113, H.117, H.123 Ligands: HAE.25 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.113, D:H.117, D:H.123, HAE.25 ZN.28: 4 residues within 4Å: Chain D: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.63, D:D.65, D:H.78, D:H.91 ZN.35: 4 residues within 4Å: Chain E: H.113, H.117, H.123 Ligands: HAE.33 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.113, E:H.117, E:H.123, HAE.33 ZN.36: 4 residues within 4Å: Chain E: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.63, E:D.65, E:H.78, E:H.91 ZN.43: 4 residues within 4Å: Chain F: H.113, H.117, H.123 Ligands: HAE.41 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.113, F:H.117, F:H.123, HAE.41 ZN.44: 4 residues within 4Å: Chain F: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.63, F:D.65, F:H.78, F:H.91

24 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.70, A:G.71, A:G.73, A:I.75, A:D.93, A:E.96 CA.6: 5 residues within 4Å: Chain A: D.53, G.85, I.86, G.87, D.89 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.53, A:G.85, A:G.87, A:D.89, H2O.2 CA.7: 4 residues within 4Å: Chain A: T.17, D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.19, A:D.19, A:E.94, A:E.94, A:E.96 CA.8: 5 residues within 4Å: Chain A: H.67 Chain B: H.67 Chain C: H.67 Ligands: CA.16, CA.24 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:H.67, A:H.67, C:H.67 CA.13: 6 residues within 4Å: Chain B: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.70, B:G.71, B:G.73, B:I.75, B:D.93, B:E.96 CA.14: 5 residues within 4Å: Chain B: D.53, G.85, I.86, G.87, D.89 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.53, B:G.85, B:G.87, B:D.89, H2O.6 CA.15: 4 residues within 4Å: Chain B: T.17, D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.19, B:D.19, B:E.94, B:E.94, B:E.96 CA.16: 5 residues within 4Å: Chain A: H.67 Chain B: H.67 Chain C: H.67 Ligands: CA.8, CA.24 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:H.67, B:H.67, A:H.67 CA.21: 6 residues within 4Å: Chain C: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.70, C:G.71, C:G.73, C:I.75, C:D.93, C:E.96 CA.22: 5 residues within 4Å: Chain C: D.53, G.85, I.86, G.87, D.89 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.53, C:G.85, C:G.87, C:D.89, H2O.10 CA.23: 4 residues within 4Å: Chain C: T.17, D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.19, C:D.19, C:E.94, C:E.94, C:E.96 CA.24: 5 residues within 4Å: Chain A: H.67 Chain B: H.67 Chain C: H.67 Ligands: CA.8, CA.16 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:H.67, B:H.67, A:H.67 CA.29: 6 residues within 4Å: Chain D: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.70, D:G.71, D:G.73, D:I.75, D:D.93, D:E.96 CA.30: 5 residues within 4Å: Chain D: D.53, G.85, I.86, G.87, D.89 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.53, D:G.85, D:G.87, D:D.89, H2O.14 CA.31: 4 residues within 4Å: Chain D: T.17, D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.19, D:D.19, D:E.94, D:E.94, D:E.96 CA.32: 5 residues within 4Å: Chain D: H.67 Chain E: H.67 Chain F: H.67 Ligands: CA.40, CA.48 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Metal complexes: F:H.67, D:H.67, E:H.67 CA.37: 6 residues within 4Å: Chain E: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain E Metal complexes: E:D.70, E:G.71, E:G.73, E:I.75, E:D.93, E:E.96 CA.38: 5 residues within 4Å: Chain E: D.53, G.85, I.86, G.87, D.89 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.53, E:G.85, E:G.87, E:D.89, H2O.17 CA.39: 4 residues within 4Å: Chain E: T.17, D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.19, E:D.19, E:E.94, E:E.94, E:E.96 CA.40: 5 residues within 4Å: Chain D: H.67 Chain E: H.67 Chain F: H.67 Ligands: CA.32, CA.48 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Metal complexes: F:H.67, D:H.67, E:H.67 CA.45: 6 residues within 4Å: Chain F: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain F Metal complexes: F:D.70, F:G.71, F:G.73, F:I.75, F:D.93, F:E.96 CA.46: 5 residues within 4Å: Chain F: D.53, G.85, I.86, G.87, D.89 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.53, F:G.85, F:G.87, F:D.89, H2O.21 CA.47: 4 residues within 4Å: Chain F: T.17, D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.19, F:D.19, F:E.94, F:E.94, F:E.96 CA.48: 5 residues within 4Å: Chain D: H.67 Chain E: H.67 Chain F: H.67 Ligands: CA.32, CA.40 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain D Metal complexes: F:H.67, E:H.67, D:H.67

Links

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Citation

Morales, R. et al., Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12. J. Mol. Biol. (2004)

Release Date

2004-12-15

Peptides

MACROPHAGE METALLOELASTASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

MACROPHAGE METALLOELASTASE

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