2YEG | pdb_00002yeg

HSP90 inhibitors and drugs from fragment and virtual screening

PDB DOI: https://doi.org/10.2210/pdb2YEG/pdb

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

Deposited: 2011-03-25 Released: 2011-06-15
Deposition Author(s): Roughley, S.D., Hubbard, R.E., Baker, L.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.324 (Depositor), 0.318 (DCC)
R-Value Work:
0.231 (Depositor), 0.229 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

How Well Can Fragments Explore Accessed Chemical Space? a Case Study from Heat Shock Protein 90.

Roughley, S.D., Hubbard, R.E.

(2011) J Med Chem 54: 3989

PubMed: 21561141 Search on PubMed
DOI: https://doi.org/10.1021/jm200350g
Primary Citation Related Structures:
2YE2, 2YE3, 2YE4, 2YE5, 2YE6, 2YE7, 2YE8, 2YE9, 2YEA, 2YEB, 2YEC, 2YED, 2YEE, 2YEF, 2YEG, 2YEH, 2YEI, 2YEJ

Organizational Affiliation

Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge, CB21 6GB, UK.

Macromolecule Content

Total Structure Weight: 57.21 kDa
Atom Count: 3,530
Modeled Residue Count: 418
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP 90-ALPHA	A, B	252	Homo sapiens	Mutation(s): 0 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900 Go to UniProtKB: P07900
PHAROS: P07900 GTEx: ENSG00000080824
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XQG Query on XQG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	6-METHYLSULFANYL-9H-PURINE C₆ H₆ N₄ S UIJIQXGRFSPYQW-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.324 (Depositor), 0.318 (DCC)
R-Value Work: 0.231 (Depositor), 0.229 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.16	α = 90
b = 89.032	β = 90
c = 98.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-15
Type: Initial release
Version 1.1: 2011-06-23
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.