Biological Assembly 1

Protein Symmetry: Asymmetric (View in 3D)

Protein Stoichiometry: Monomer

Biological Assembly 2

Protein Symmetry: C1 (View in 3D)

Protein Stoichiometry: A

Macromolecule Content

• Unique protein chains: 1

4H3X

Crystal structure of an MMP broad spectrum hydroxamate based inhibitor CC27 in complex with the MMP-9 catalytic domain

• DOI: 10.2210/pdb4h3x/pdb

• Classification: HYDROLASE / HYDROLASE Inhibitor
• Deposited: 2012-09-14 Released: 2013-04-24
• Deposition author(s): Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.
• Organism: Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1

Structural Biology Knowledgebase: 4H3X

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.254
• R-Value Work: 0.196

wwPDB Validation Full Report

Literature

Macromolecules

Classification: HYDROLASE / HYDROLASE Inhibitor

Total Structure Weight: 38840.80

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
10B	A, B	N-2-(biphenyl-4-ylsulfonyl)-N-2-(isopropyloxy)- acetohydroxamic acid N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~- (propan-2-yloxy)glycinamide (Synonym) C17 H20 N2 O5 S PHGLPDURIUEELR-UHFFFAOYSA-N	Poseview Image of 10B in 4H3X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer   Binding Pocket (JSmol)   Electron Density (JSmol)
PEG	B	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N	Poseview Image of PEG in 4H3X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer   Binding Pocket (JSmol)   Electron Density (JSmol)
GOL	A, B	GLYCEROL 2, (Synonym) C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N	Poseview Image of GOL in 4H3X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer   Binding Pocket (JSmol)   Electron Density (JSmol)
PGO	A	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N	Poseview Image of PGO in 4H3X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer   Binding Pocket (JSmol)   Electron Density (JSmol)
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N	Poseview Image of ZN in 4H3X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer   Binding Pocket (JSmol)   Electron Density (JSmol)
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N	Poseview Image of CA in 4H3X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer   Binding Pocket (JSmol)   Electron Density (JSmol)

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
10B	IC50: 200 nM (90) BindingDB N/A in BindingMoad N/A in PDBbind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.254
• R-Value Work: 0.196
• Space Group: P 1 2₁ 1
• Electron Density Server: EDS

Unit Cell:

Length (Å)	Angle (°)
a = 40.11	α = 90.00
b = 97.94	β = 111.73
c = 46.08	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2012-09-14
• Released Date: 2013-04-24
• Deposition author(s): Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.

Revision History

• 2015-08-12
  Type: Citation | Details: Citation update
• 2014-10-08
  Type: Citation | Details: --
• 2013-05-01
  Type: Citation | Details: --