1G4K

X-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

• PDB DOI: https://doi.org/10.2210/pdb1G4K/pdb

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


• Deposited: 2000-10-27 Released: 2001-04-25 
• Deposition Author(s): Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.244 

Literature

X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin.

Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

(2001) Protein Sci 10: 923-926

• PubMed: 11316871 
• DOI: https://doi.org/10.1110/ps.48401
• Primary Citation of Related Structures:  
  1G4K


• PubMed Abstract: 
  

  A new class of matrix metalloproteinase (MMP) inhibitors has been identified by screening a collection of compounds against stromelysin. The inhibitors, 2,4,6-pyrimidine triones, have proven to be potent inhibitors of gelatinases A and B. An X-ray crystal structure of one representative compound bound to the catalytic domain of stromelysin shows that the compounds bind at the active site and ligand the active-site zinc. The pyrimidine triones mimic substrates in forming hydrogen bonds to key residues in the active site, and provide opportunities for placing appropriately chosen groups into the S1' specificity pocket of MMPS: A number of compounds have been synthesized and assayed against stromelysin, and the variations in potency are explained in terms of the binding mode revealed in the X-ray crystal structure.

---

Organizational Affiliation: 

Roche Research Center, Hoffmann-La Roche Inc., Nutley, New Jersey 07110, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.44 kDa 
• Atom Count: 4,294 
• Modelled Residue Count: 504 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1	A, B, C	168	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HQQ	I [auth A], O [auth B], V [auth C]	5-METHYL-5-(4-PHENOXY-PHENYL)-PYRIMIDINE-2,4,6-TRIONE C17 H14 N2 O4 RTBMLCLTYAPKIF-UHFFFAOYSA-N
GOL	P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], J [auth B], K [auth B], Q [auth C], R [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], S [auth C], T [auth C], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HQQ	BindingDB:  1G4K	IC50: 2000 (nM) from 1 assay(s)
	PDBBind:  1G4K	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.244 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.8	α = 90
b = 103.8	β = 90
c = 147.49	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-25 
Deposition Author(s): Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

Revision History  

• Version 1.0: 2001-04-25
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection, Database references
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations