Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.90 kDa 
• Atom Count: 1471 
• Modelled Residue Count: 160 
• Deposited Residue Count: 160 
• Unique protein chains: 1

1HFS

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-764,004

• DOI: 10.2210/pdb1HFS/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-02-13 Released: 1998-02-18 
• Deposition Author(s): Becker, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

Inhibition of stromelysin-1 (MMP-3) by P1'-biphenylylethyl carboxyalkyl dipeptides.

Esser, C.K., Bugianesi, R.L., Caldwell, C.G., Chapman, K.T., Durette, P.L., Girotra, N.N., Kopka, I.E., Lanza, T.J., Levorse, D.A., MacCoss, M., Owens, K.A., Ponpipom, M.M., Simeone, J.P., Harrison, R.K., Niedzwiecki, L., Becker, J.W., Marcy, A.I., Axel, M.G., Christen, A.J., McDonnell, J., Moore, V.L., Olszewski, J.M., Saphos, C., Visco, D.M., Shen, F., Colletti, A., Krieter, P.A., Hagmann, W.K.

(1997) J Med Chem 40: 1026-1040

• PubMed: 9083493 
• DOI: 10.1021/jm960465t
• Primary Citation of Related Structures:  
  1HFS


• PubMed Abstract: 
  

Carboxyalkyl peptides containing a biphenylylethyl group at the P1' position were found to be potent inhibitors of stromelysin-1 (MMP-3) and gelatinase A (MMP-2), in the range of 10-50 nM, but poor inhibitors of collagenase (MMP-1). Combination of a biphenylylethyl moiety at P1', a tert-butyl group at P2', and a methyl group at P3' produced orally bioavailable inhibitors as measured by an in vivo model of MMP-3 degradation of radiolabeled transferrin in the mouse pleural cavity. The X-ray structure of a complex of a P1-biphenyl inhibitor and the catalytic domain of MMP-3 is described. Inhibitors that contained halogenated biphenylylethyl residues at P1' proved to be superior in terms of enzyme potency and oral activity with 2(R)-[2-(4'-fluoro-4-biphenylyl)ethyl]-4(S)-n-butyl-1,5-pentane dioic acid 1-(alpha(S)-tert-butylglycine methylamide) amide (L-758,354, 26) having a Ki of 10 nM against MMP-3 and an ED50 of 11 mg/kg po in the mouse pleural cavity assay. This compound was evaluated in acute (MMP-3 and IL-1 beta injection in the rabbit) and chronic (rat adjuvant-induced arthritis and mouse collagen-induced arthritis) models of cartilage destruction but showed activity only in the MMP-3 injection model (ED50 = 6 mg/kg iv).

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Related Citations: 

• Comparison of the Structure of Human Recombinant Short Form Stromelysin by Multidimensional Heteronuclear NMR and X-Ray Crystallography
  Gooley, P.R., O'Connell, J.F., Marcy, A.I., Cuca, G.C., Axel, M.G., Caldwell, C.G., Hagmann, W.K., Becker, J.W.
  (1996) J Biomol NMR 7: 8

• Stromelysin-1: Three-Dimensional Structure of the Inhibited Catalytic Domain and of the C-Truncated Proenzyme
  Becker, J.W., Marcy, A.I., Rokosz, L.L., Axel, M.G., Burbaum, J.J., Fitzgerald, P.M., Cameron, P.M., Esser, C.K., Hagmann, W.K., Hermes, J.D., Springer, J.P.
  (1995) Protein Sci 4: 1966

• The NMR Structure of the Inhibited Catalytic Domain of Human Stromelysin-1
  Gooley, P.R., O'Connell, J.F., Marcy, A.I., Cuca, G.C., Salowe, S.P., Bush, B.L., Hermes, J.D., Esser, C.K., Hagmann, W.K., Springer, J.P., Johnson, B.A.
  (1994) Nat Struct Biol 1: 111

• Inhibition of Matrix Metalloproteinases by N-Carboxyalkyl Peptides
  Chapman, K.T., Kopka, I.E., Durette, P.L., Esser, C.K., Lanza, T.J., Izquierdo-Martin, M., Niedzwiecki, L., Chang, B., Harrison, R.K., Kuo, D.W., Lin, T.Y., Stein, R.L., Hagmann, W.K.
  (1993) J Med Chem 36: 4293

• Human Fibroblast Stromelysin Catalytic Domain: Expression, Purification, and Characterization of a C-Terminally Truncated Form
  Marcy, A.I., Eiberger, L.L., Harrison, R., Chan, H.K., Hutchinson, N.I., Hagmann, W.K., Cameron, P.M., Boulton, D.A., Hermes, J.D.
  (1991) Biochemistry 30: 6476

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065-0900, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1	A	160	Homo sapiens	Mutation(s): 0  Gene Names: MMP3, STMY1 EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens) Explore P08254  Go to UniProtKB:  P08254
PHAROS:  P08254 GTEx:  ENSG00000149968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L04	G [auth A]	6-(4'-FLUORO-BIPHENYL-4-YL)-4-(3-METHYL-1-PHENYLCARBAMOYL-BUTYLCARBAMOYL)-2-[4-(1-OXO-1,3-DIHYDRO-ISOINDOL-2-YL)-BUTYL]-HEXANOIC ACID C43 H48 F N3 O5 WSHMSPGZDPZGRV-GZYXPWJKSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
L04	Ki :  2   nM  PDBBind
L04	Ki:  2   nM  BindingDB
L04	Ki:  2   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.14	α = 90
b = 85.35	β = 90
c = 55.26	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-02-13 
• Released Date: 1998-02-18 
Deposition Author(s): Becker, J.W.

Revision History  

• Version 1.0: 1998-02-18
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-22
  Changes: Database references
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other