1O46

CRYSTAL STRUCTURE OF SH2 IN COMPLEX WITH RU90395.

DOI: 10.2210/pdb1O46/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-06-15 Released: 2004-02-17
Deposition Author(s): Lange, G., Loenze, P., Liesum, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.192
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Requirements for specific binding of low affinity inhibitor fragments to the SH2 domain of (pp60)Src are identical to those for high affinity binding of full length inhibitors.

Lange, G., Lesuisse, D., Deprez, P., Schoot, B., Loenze, P., Benard, D., Marquette, J.P., Broto, P., Sarubbi, E., Mandine, E.

(2003) J Med Chem 46: 5184-5195

PubMed: 14613321 Search on PubMed
DOI: 10.1021/jm020970s
Primary Citation of Related Structures:
1O4A, 1O45, 1O44, 1O43, 1O42, 1O41, 1O4M, 1O4L, 1O4K, 1O4J

PubMed Abstract:

Results from a novel approach which uses protein crystallography for the screening of a low affinity inhibitor fragment library are analyzed by comparing the X-ray structures with bound fragments to the structures with the corresponding full length inhibitors. The screen for new phospho-tyrosine mimics binding to the SH2 domain of (pp60)src was initiated because of the limited cell penetration of phosphates. Fragments in our library typically had between 6 and 30 atoms and included compounds which had either millimolar activity in a Biacore assay or were suggested by the ab initio design program LUDI but had no measurable affinity. All identified fragments were located in the phospho-tyrosine pocket. The most promising fragments were successfully used to replace the phospho-tyrosine and resulted in novel nonpeptidic high affinity inhibitors. The significant diversity of successful fragments is reflected in the high flexibility of the phospho-tyrosine pocket. Comparison of the X-ray structures shows that the presence of the H-bond acceptors and not their relative position within the pharmacophore are essential for fragment binding and/or high affinity binding of full length inhibitors. The X-ray data show that the fragments are recognized by forming a complex H-bond network within the phospho-tyrosine pocket of SH2. No fragment structure was found in which this H-bond network was incomplete, and any uncompensated H-bond within the H-bond network leads to a significant decrease in the affinity of full length inhibitors. No correlation between affinity and fragment binding was found for these polar fragments and hence affinity-based screening would have overlooked some interesting starting points for inhibitor design. In contrast, we were unable to identify electron density for hydrophobic fragments, confirming that hydrophobic interactions are important for inhibitor affinity but of minor importance for ligand recognition. Our results suggest that a screening approach using protein crystallography is particularly useful to identify universal fragments for the conserved hydrophilic recognition sites found in target families such as SH2 domains, phosphatases, kinases, proteases, and esterases.

Organizational Affiliation:

Aventis Pharma, 102 route de Noisy, 93235 Romainville, France. gudrum.lange@Bayercropscience.com

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC	A	108	Homo sapiens	Mutation(s): 0 Gene Names: SRC, SRC1 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P12931 (Homo sapiens) Explore P12931 Go to UniProtKB: P12931
NIH Common Fund Data Resources
PHAROS: P12931 GTEx: ENSG00000197122
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
903 Query on 903 Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	2-{4-[2-ACETYLAMINO-2-(1-BIPHENYL-4-YLMETHYL-2-OXO-AZEPAN-3-YLCARBAMOYL)-ETHYL]-2-METHOXYCARBONYL-PHENYL}-2-FLUORO-MALONIC ACID C₃₅ H₃₆ F N₃ O₉ RLLAUERCSKPFGD-VMPREFPWSA-N		Ligand Interaction