7MPH | pdb_00007mph

GRB2 SH2 Domain with Compound 7

PDB DOI: https://doi.org/10.2210/pdb7MPH/pdb

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

Deposited: 2021-05-04 Released: 2021-09-22
Deposition Author(s): Sun, L., Schonbrunn, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.277 (Depositor), 0.276 (DCC)
R-Value Work:
0.231 (Depositor), 0.235 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Synthesis and structural characterization of a monocarboxylic inhibitor for GRB2 SH2 domain.

Xiao, T., Sun, L., Zhang, M., Li, Z., Haura, E.B., Schonbrunn, E., Ji, H.

(2021) Bioorg Med Chem Lett 51: 128354-128354

PubMed: 34506932 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bmcl.2021.128354
Primary Citation Related Structures:
7MPH

PubMed Abstract:
A monocarboxylic inhibitor was designed and synthesized to disrupt the protein-protein interaction (PPI) between GRB2 and phosphotyrosine-containing proteins. Biochemical characterizations show compound 7 binds with the Src homology 2 (SH2) domain of GRB2 and is more potent than EGFR ₁₀₆₈ phosphopeptide 14-mer. X-ray crystallographic studies demonstrate compound 7 occupies the GRB2 binding site for phosphotyrosine-containing sequences and reveal key structural features for GRB2-inhibitor binding. This compound with a -1 formal charge offers a new direction for structural optimization to generate cell-permeable inhibitors for this key protein target of the aberrant Ras-MAPK signaling cascade.

Organizational Affiliation

Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States.

Macromolecule Content

Total Structure Weight: 71.83 kDa
Atom Count: 4,976
Modeled Residue Count: 563
Deposited Residue Count: 570
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A, B, C, D, E A, B, C, D, E, F	95	Homo sapiens	Mutation(s): 0 Gene Names: GRB2, ASH
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62993
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZLY (Subject of Investigation/LOI) Query on ZLY Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain Y [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	CA [auth E] FA [auth F] G [auth A] L [auth B] R [auth C] CA [auth E], FA [auth F], G [auth A], L [auth B], R [auth C], Y [auth D]	(4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid C₃₈ H₄₄ N₄ O₆ ZYRZDVCTSBJOQD-GZNVFMSSSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain Y [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain Z [auth D] SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] I [auth A] J [auth A] K [auth A] AA [auth D], BA [auth D], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], X [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain JA [auth F] SDF format, chain IA [auth F] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain JA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain JA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E]	DA [auth E] EA [auth E] GA [auth F] H [auth A] HA [auth F] DA [auth E], EA [auth E], GA [auth F], H [auth A], HA [auth F], IA [auth F], JA [auth F], M [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]