1BQO | pdb_00001bqo

DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS

• PDB DOI: https://doi.org/10.2210/pdb1BQO/pdb

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


• Deposited: 1998-08-17 Released: 1999-08-17 
• Deposition Author(s): Pikul, S., Dunham, K.L.M., Almstead, N.G., De, B., Natchus, M.G., Anastasio, M.V., Mcphail, S.J., Snider, C.E., Taiwo, Y.O., Rydel, T.J., Dunaway, C.M., Gu, F., Mieling, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.294 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Discovery of potent, achiral matrix metalloproteinase inhibitors.

Pikul, S., McDow Dunham, K.L., Almstead, N.G., De, B., Natchus, M.G., Anastasio, M.V., McPhail, S.J., Snider, C.E., Taiwo, Y.O., Rydel, T., Dunaway, C.M., Gu, F., Mieling, G.E.

(1998) J Med Chem 41: 3568-3571

• PubMed: 9733482 
• DOI: https://doi.org/10.1021/jm980253r
• Primary Citation Related Structures: 
  1BQO

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Organizational Affiliation: 
• Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Road, Mason, Ohio 45040, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 39.85 kDa 
• Atom Count: 2,841 
• Modeled Residue Count: 342 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1	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
N25	M [auth B]	1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHYDRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE C21 H27 N3 O8 S2 MCSWSPNUKWMZHM-UHFFFAOYSA-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
N25	BindingDB:  1BQO	Ki: 18 (nM) from 1 assay(s)
		IC50: min: 18, max: 28.6 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.294 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.9	α = 90
b = 79	β = 90
c = 106.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-17 
Deposition Author(s): Pikul, S., Dunham, K.L.M., Almstead, N.G., De, B., Natchus, M.G., Anastasio, M.V., Mcphail, S.J., Snider, C.E., Taiwo, Y.O., Rydel, T.J., Dunaway, C.M., Gu, F., Mieling, G.E.

Revision History  

• Version 1.0: 1999-08-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other