3LKA

Catalytic domain of human MMP-12 complexed with hydroxamic acid and paramethoxy-sulfonyl amide

• PDB DOI: https://doi.org/10.2210/pdb3LKA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-01-27 Released: 2010-05-12 
• Deposition Author(s): Calderone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Entropic contribution to the linking coefficient in fragment based drug design: a case study.

Borsi, V., Calderone, V., Fragai, M., Luchinat, C., Sarti, N.

(2010) J Med Chem 53: 4285-4289

• PubMed: 20415416 
• DOI: https://doi.org/10.1021/jm901723z
• Primary Citation of Related Structures:  
  3LKA


• PubMed Abstract: 
  

  For several drug leads obtained by tethering weak binding ligands, the dissociation constant is smaller than the product of those of the individual fragments by a factor named the linking coefficient, E. This favorable contribution is attributed to the entropic gain that is realized when two weak binding ligands are tethered. Here we show a case study where the linking coefficient is strikingly small (E = 2.1 x 10(-3) M(-1)) and its totally entropic nature is demonstrated.

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Organizational Affiliation: 

Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.

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 kDa 
• Atom Count: 1,396 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	158	Homo sapiens	Mutation(s): 1  Gene Names: HME, MMP12 EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
PHAROS:  P39900 GTEx:  ENSG00000262406

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M4S	H [auth A]	4-methoxybenzenesulfonamide C7 H9 N O3 S MSFQEZBRFPAFEX-UHFFFAOYSA-N
HAE	G [auth A]	ACETOHYDROXAMIC ACID C2 H5 N O2 RRUDCFGSUDOHDG-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M4S	PDBBind:  3LKA	Kd: 1.50e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.566	α = 90
b = 60.194	β = 115.09
c = 54.215	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Calderone, V.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description