1BIW

DESIGN AND SYNTHESIS OF CONFORMATIONALLY-CONSTRAINED MMP INHIBITORS

• PDB DOI: https://doi.org/10.2210/pdb1BIW/pdb

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


• Deposited: 1998-06-19 Released: 1999-07-16 
• Deposition Author(s): Natchus, M.G., Cheng, M., Wahl, C.T., Pikul, S., Almstead, N.G., Bradley, R.S., Taiwo, Y.O., Mieling, G.E., Dunaway, C.M., Snider, C.E., McIver, J.M., Barnett, B.L., McPhail, S.J., Anastasio, M.B., De, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Literature

Design and synthesis of conformationally-constrained MMP inhibitors.

Natchus, M.G., Cheng, M., Wahl, C.T., Pikul, S., Almstead, N.G., Bradley, R.S., Taiwo, Y.O., Mieling, G.E., Dunaway, C.M., Snider, C.E., McIver, J.M., Barnett, B.L., McPhail, S.J., Anastasio, M.B., De, B.

(1998) Bioorg Med Chem Lett 8: 2077-2080

• PubMed: 9873489 
• DOI: https://doi.org/10.1016/s0960-894x(98)00370-9
• Primary Citation of Related Structures:  
  1BIW


• PubMed Abstract: 
  

  A novel series of conformationally constrained matrix metalloprotease inhibitors was identified. The potencies observed for these inhibitors were highly dependent upon the substitution pattern on the caprolactam ring as well as the succinate moiety.

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Organizational Affiliation: 

Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.75 kDa 
• Atom Count: 2,813 
• Modelled Residue Count: 342 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (STROMELYSIN-1 COMPLEX)	A, B	173	Homo sapiens	Mutation(s): 0  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
S80	M [auth B]	N1-HYDROXY-2-(3-HYDROXY-PROPYL)-3-ISOBUTYL-N4-[1-(2-METHOXY-ETHYL)-2-OXO-AZEPAN-3-YL]-SUCCINAMIDE C20 H37 N3 O6 JLEGVELHGVWFGG-BBWFWOEESA-N
ZN	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
S80	BindingDB:  1BIW	IC50: 104 (nM) from 1 assay(s)
	PDBBind:  1BIW	IC50: 104 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.06	α = 90
b = 77.28	β = 90
c = 106.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-16 
Deposition Author(s): Natchus, M.G., Cheng, M., Wahl, C.T., Pikul, S., Almstead, N.G., Bradley, R.S., Taiwo, Y.O., Mieling, G.E., Dunaway, C.M., Snider, C.E., McIver, J.M., Barnett, B.L., McPhail, S.J., Anastasio, M.B., De, B.

Revision History  

• Version 1.0: 1999-07-16
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations