1DB4 | pdb_00001db4

HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8

• PDB DOI: https://doi.org/10.2210/pdb1DB4/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1999-11-02 Released: 1999-11-12 
• Deposition Author(s): Chirgadze, N.Y., Schevitz, R.W., Wery, J.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.256 (Depositor) 
• R-Value Work: 
  0.226 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2.

Schevitz, R.W., Bach, N.J., Carlson, D.G., Chirgadze, N.Y., Clawson, D.K., Dillard, R.D., Draheim, S.E., Hartley, L.W., Jones, N.D., Mihelich, E.D., Olkowski, J.L., Snyder, D.W., Sommers, C., Wery, J.-P.

(1995) Nat Struct Biol 2: 458-465

• PubMed: 7664108 
• DOI: https://doi.org/10.1038/nsb0695-458
• Primary Citation Related Structures: 
  1DB4, 1DB5, 1DCY


• PubMed Abstract: 
  

  A lead compound obtained from a high volume human non-pancreatic secretory phospholipase A2 (hnps-PLA2) screen has been developed into a potent inhibitor using detailed structural knowledge of inhibitor binding to the enzyme active site. Four crystal structures of hnps-PLA2 complexed with a series of increasingly potent indole inhibitors were determined and used as the structural basis for both understanding this binding and providing valuable insights for further development. The application of structure-based drug design has made possible improvements in the binding of this screening lead to the enzyme by nearly three orders of magnitude. Furthermore, the optimized structure (LY311727) displayed 1,500-fold selectivity when assayed against porcine pancreatic s-PLA2.

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Organizational Affiliation: 
• Lilly Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.44 kDa 
• Atom Count: 1,066 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	A	124	Homo sapiens	Mutation(s): 0  EC: 3.1.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P14555 (Homo sapiens) Explore P14555  Go to UniProtKB:  P14555
PHAROS:  P14555 GTEx:  ENSG00000188257

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8IN	D [auth A]	[3-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-PROPYL-]-PHOSPHONIC ACID C21 H25 N2 O5 P AQEYCNKFBRLUOT-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8IN	BindingDB:  1DB4	IC50: min: 57, max: 6.70e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.256 (Depositor) 
• R-Value Work:  0.226 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.012	α = 90
b = 77.012	β = 90
c = 91.62	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-12 
Deposition Author(s): Chirgadze, N.Y., Schevitz, R.W., Wery, J.-P.

Revision History  

• Version 1.0: 1999-11-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary