3LGP | pdb_00003lgp

Crystal structure of catalytic domain of tace with benzimidazolyl-thienyl-tartrate based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LGP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2010-01-21 Released: 2010-07-28 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 

Literature

Structure and activity relationships of tartrate-based TACE inhibitors.

Li, D., Popovici-Muller, J., Belanger, D.B., Caldwell, J., Dai, C., David, M., Girijavallabhan, V.M., Lavey, B.J., Lee, J.F., Liu, Z., Mazzola, R., Rizvi, R., Rosner, K.E., Shankar, B., Spitler, J., Ting, P.C., Vaccaro, H., Yu, W., Zhou, G., Zhu, Z., Niu, X., Sun, J., Guo, Z., Orth, P., Chen, S., Kozlowski, J.A., Lundell, D.J., Madison, V., McKittrick, B., Piwinski, J.J., Shih, N.Y., Shipps, G.W., Siddiqui, M.A., Strickland, C.O.

(2010) Bioorg Med Chem Lett 20: 4812-4815

• PubMed: 20638281 
• DOI: https://doi.org/10.1016/j.bmcl.2010.06.104
• Primary Citation of Related Structures:  
  3LGP


• PubMed Abstract: 
  

  The syntheses and structure-activity relationships of the tartrate-based TACE inhibitors are discussed. The optimization of both the prime and non-prime sites led to compounds with picomolar activity. Several analogs demonstrated good rat pharmacokinetics.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, Cambridge, 320 Bent Street, Cambridge, MA 02141, United States. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.48 kDa 
• Atom Count: 4,209 
• Modelled Residue Count: 505 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin and metalloproteinase domain-containing protein 17	A, B	270	Homo sapiens	Mutation(s): 3  Gene Names: ADAM17, CSVP, TACE EC: 3.4.24.86
UniProt & NIH Common Fund Data Resources
Find proteins for P78536 (Homo sapiens) Explore P78536  Go to UniProtKB:  P78536
PHAROS:  P78536 GTEx:  ENSG00000151694

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
50X	D [auth A], F [auth B]	(2R,3R)-4-[(2R)-2-(3-chlorophenyl)pyrrolidin-1-yl]-2,3-dihydroxy-4-oxo-N-[(5-{[2-(trifluoromethyl)-1H-benzimidazol-1-yl]methyl}thiophen-2-yl)methyl]butanamide C28 H26 Cl F3 N4 O4 S JSNHRUZOJTYCCL-GMKZXUHWSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
50X	BindingDB:  3LGP	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.344	α = 90
b = 76.618	β = 90
c = 103.506	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Orth, P.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary