Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.43 kDa 
• Atom Count: 1274 
• Modelled Residue Count: 157 
• Deposited Residue Count: 169 
• Unique protein chains: 1

3AYK

CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH CGS-27023A, NMR, MINIMIZED AVERAGE STRUCTURE

• PDB DOI: 10.2210/pdb3AYK/pdb

• Classification: MATRIX METALLOPROTEINASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-02-01 Released: 1999-06-07 
• Deposition Author(s): Powers, R., Moy, F.J.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: LOWEST ENERGY, LOWEST VIOLATIONS, CONSISTENT FOLD 

Literature

NMR solution structure of the catalytic fragment of human fibroblast collagenase complexed with a sulfonamide derivative of a hydroxamic acid compound.

Moy, F.J., Chanda, P.K., Chen, J.M., Cosmi, S., Edris, W., Skotnicki, J.S., Wilhelm, J., Powers, R.

(1999) Biochemistry 38: 7085-7096

• PubMed: 10353819 
• DOI: 10.1021/bi982576v
• Primary Citation of Related Structures:  
  3AYK, 4AYK


• PubMed Abstract: 
  

The solution structure of the catalytic fragment of human fibroblast collagenase (MMP-1) complexed with a sulfonamide derivative of a hydroxamic acid compound (CGS-27023A) has been determined using two-dimensional and three-dimensional heteronuclear NMR spectroscopy. The solution structure of the complex was calculated by means of hybrid distance geometry-simulated annealing using a combination of experimental NMR restraints obtained from the previous refinement of the inhibitor-free MMP-1 (1) and recent restraints for the MMP-1:CGS-27023A complex. The hydroxamic acid moiety of CGS-27023A was found to chelate to the "right" of the catalytic zinc where the p-methoxyphenyl sits in the S1' active-site pocket, the isopropyl group is in contact with H83 and N80, and the pyridine ring is solvent exposed. The sulfonyl oxygens are in hydrogen-bonding distance to the backbone NHs of L81 and A82. This is similar to the conformation determined by NMR of the inhibitor bound to stromelysin (2, 3). A total of 48 distance restraints were observed between MMP-1 and CGS-27023A from 3D 13C-edited/12C-filtered NOESY and 3D 15N-edited NOESY experiments. An additional 18 intramolecular restraints were observed for CGS-27023A from a 2D 12C-filtered NOESY experiment. A minimal set of NMR experiments in combination with the free MMP-1 assignments were used to assign the MMP-1 (1)H, 13C, and 15N resonances in the MMP-1:CGS-27023A complex. The assignments of CGS-27023A in the complex were obtained from 2D 12C-filtered NOESY and 2D 12C-filtered TOCSY experiments.

---

Related Citations: 

• High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR.
  Moy, F.J., Chanda, P.K., Cosmi, S., Pisano, M.R., Urbano, C., Wilhelm, J., Powers, R.
  (1998) Biochemistry 37: 1495

• Assignments, secondary structure and dynamics of the inhibitor-free catalytic fragment of human fibroblast collagenase.
  Moy, F.J., Pisano, M.R., Chanda, P.K., Urbano, C., Killar, L.M., Sung, M.L., Powers, R.
  (1997) J Biomol NMR 10: 9

---

Organizational Affiliation: 

Department of Structural Biology, Wyeth-Ayerst Research, Pearl River, New York 10965, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLLAGENASE)	A	169	Homo sapiens	Mutation(s): 0  Gene Names: MMP1, CLG EC: 3.4.24.7
UniProt & NIH Common Fund Data Resources
Find proteins for P03956 (Homo sapiens) Explore P03956  Go to UniProtKB:  P03956
PHAROS:  P03956

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CGS	E [auth A]	N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE C18 H23 N3 O5 S BSIZUMJRKYHEBR-QGZVFWFLSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CGS	BindingDB:  3AYK	Ki: 33 (nM) from 1 assay(s)
		IC50: min: 2.5, max: 96 (nM) from 10 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: LOWEST ENERGY, LOWEST VIOLATIONS, CONSISTENT FOLD 
• OLDERADO: 3AYK Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-01 
• Released Date: 1999-06-07 
Deposition Author(s): Powers, R., Moy, F.J.

Revision History  

• Version 1.0: 1999-06-07
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-30
  Changes: Data collection, Database references, Derived calculations