Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.97 kDa 
• Atom Count: 1,688 
• Modelled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

 4XCT

Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) in complex with the MMP-9 catalytic domain.

• PDB DOI:  https://doi.org/10.2210/pdb4XCT/pdb

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


• Deposited: 2014-12-18 Released: 2015-04-22 
• Deposition Author(s): Stura, E.A., Tepshi, L., Nuti, E., Dive, V., Cassar-Lajeunesse, E., Vera, L., Rossello, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Literature

N-O-Isopropyl Sulfonamido-Based Hydroxamates as Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity.

Nuti, E., Cantelmo, A.R., Gallo, C., Bruno, A., Bassani, B., Camodeca, C., Tuccinardi, T., Vera, L., Orlandini, E., Nencetti, S., Stura, E.A., Martinelli, A., Dive, V., Albini, A., Rossello, A.

(2015) J Med Chem 58: 7224-7240

• PubMed: 26263024 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00367
• Primary Citation of Related Structures:  
  4WZV, 4XCT


• PubMed Abstract: 
  

Matrix metalloproteinases (MMPs) have been shown to be involved in tumor-induced angiogenesis. In particular, MMP-2, MMP-9, and MMP-14 have been reported to be crucial for tumor angiogenesis and the formation of metastasis, thus becoming attractive targets in cancer therapy. Here, we report our optimization effort to identify novel N-isopropoxy-arylsulfonamide hydroxamates with improved inhibitory activity toward MMP-2, MMP-9, and MMP-14 with respect to the previously discovered compound 1. A new series of hydroxamates was designed, synthesized, and tested for their antiangiogenic activity using in vitro assays with human umbilical vein endothelial cells (HUVECs). A nanomolar MMP-2, MMP-9, and MMP-14 inhibitor was identified, compound 3, able to potently inhibit angiogenesis in vitro and also in vivo in the matrigel sponge assay in mice. Finally, X-ray crystallographic and docking studies were conducted for compound 3 in order to investigate its binding mode to MMP-9 and MMP-14.

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Organizational Affiliation: 

Dipartimento di Farmacia, Università di Pisa , via Bonanno 6, 56126 Pisa, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix metalloproteinase-9,Matrix metalloproteinase-9	A	157	Homo sapiens	Mutation(s): 0  Gene Names: MMP9, CLG4B EC: 3.4.24.35
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens) Explore P14780  Go to UniProtKB:  P14780
PHAROS:  P14780

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N73	B [auth A]	(2~{R})-3-methyl-~{N}-oxidanylidene-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxy-amino]butanamide C20 H24 N2 O5 S JYURKDGMICGTJM-LJQANCHMSA-N
GOL	N [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BUD	Q [auth A]	(2S,3S)-butane-2,3-diol C4 H10 O2 OWBTYPJTUOEWEK-IMJSIDKUSA-N
DMS	H [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
PGO	O [auth A], P [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N73	Binding MOAD:  4XCT	IC50: 6.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.6	α = 90
b = 39.6	β = 90
c = 163.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
XDS	data reduction
Coot	model building
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Stura, E.A., Tepshi, L., Nuti, E., Dive, V., Cassar-Lajeunesse, E., Vera, L., Rossello, A.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Database references
• Version 1.2: 2015-10-07
  Changes: Database references
• Version 2.0: 2019-05-29
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary