4XCT

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


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 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Matrix metalloproteinase-9,Matrix metalloproteinase-9 A157Homo sapiensMutation(s): 0 
Gene Names: MMP9CLG4B
EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
NIH Common Fund Data Resources
PHAROS:  P14780
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N73
Query on N73

Download Ideal Coordinates CCD File 
A
(2~{R})-3-methyl-~{N}-oxidanylidene-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxy-amino]butanamide
C20 H24 N2 O5 S
JYURKDGMICGTJM-LJQANCHMSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BUD
Query on BUD

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A
(2S,3S)-butane-2,3-diol
C4 H10 O2
OWBTYPJTUOEWEK-IMJSIDKUSA-N
 Ligand Interaction
DMS
Query on DMS

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A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N73IC50:  6.699999809265137   nM  Binding MOAD
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 = 39.6α = 90
b = 39.6β = 90
c = 163.96γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
XDSdata reduction
Cootmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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