1CJ1

GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE

PDB DOI: https://doi.org/10.2210/pdb1CJ1/pdb

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

Deposited: 1999-04-21 Released: 1999-12-22
Deposition Author(s): Rahuel, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.317
R-Value Work: 0.305

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure-based design, synthesis, and X-ray crystallography of a high-affinity antagonist of the Grb2-SH2 domain containing an asparagine mimetic.

Furet, P., Garcia-Echeverria, C., Gay, B., Schoepfer, J., Zeller, M., Rahuel, J.

(1999) J Med Chem 42: 2358-2363

PubMed: 10395476 Search on PubMed
DOI: https://doi.org/10.1021/jm991013u
Primary Citation of Related Structures:
1CJ1

PubMed Abstract:
Previous efforts in the search for molecules capable of blocking the associations between the activated tyrosine kinase growth factor receptors and the SH2 domain of Grb2 had resulted in the identification of 3-amino-Z-pTyr-Ac6c-Asn-NH2, a high-affinity and selective antagonist of this SH2 domain. In the present paper, we report the successful replacement of asparagine in this compound by a beta-amino acid mimetic, which brings us closer to our objective of identifying a Grb2-SH2 antagonist suitable for pharmacological investigations.

Organizational Affiliation

Oncology Research Department, Novartis Pharma Inc., CH-4002 Basel, Switzerland. pascal.furet@pharma.novartis.com

Macromolecule Content

Total Structure Weight: 142.16 kDa
Atom Count: 10,060
Modelled Residue Count: 1,152
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	96	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens) Explore P62993 Go to UniProtKB: P62993
PHAROS: P62993 GTEx: ENSG00000177885
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62993
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C78 Query on C78 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth K] mmCIF format, chain X [auth L]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	[1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER C₃₁ H₄₂ N₅ O₉ P SLNOMHLVQNIGRT-NXCFDTQHSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Binding Affinity Annotations
ID	Source	Binding Affinity
C78	PDBBind: 1CJ1	IC50: 1.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.317
R-Value Work: 0.305
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.8	α = 90
b = 93.3	β = 90
c = 232.8	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
XDS	data reduction
AUTOMAR	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-12-22

Deposition Author(s):

Rahuel, J.

Revision History (Full details and data files)

Version 1.0: 1999-12-22
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-08-02
Changes: Database references, Derived calculations, Refinement description