2FYP | pdb_00002fyp

GRP94 in complex with the novel HSP90 Inhibitor Radester amine

PDB DOI: https://doi.org/10.2210/pdb2FYP/pdb

Classification: CHAPERONE
Organism(s): Canis lupus familiaris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-02-08 Released: 2007-02-06
Deposition Author(s): Immormino, R.M., Gewirth, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.265 (Depositor), 0.276 (DCC)
R-Value Work:
0.230 (Depositor), 0.244 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Inhibittory Ligands Adopt Different Conformations When Bound to Hsp90 or GRP94: Implications for Paralog-specific Drug Design

Immormino, R.M., Gewirth, D.T., Blagg, B.S.

To be published.

Macromolecule Content

Total Structure Weight: 55.62 kDa
Atom Count: 4,141
Modeled Residue Count: 464
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmin	A, B	236	Canis lupus familiaris	Mutation(s): 0 Gene Names: TRA1 EC: 3.6.4
UniProt
Find proteins for P41148 (Canis lupus familiaris) Explore P41148 Go to UniProtKB: P41148
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41148
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RDE Query on RDE Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	2-(3-AMINO-2,5,6-TRIMETHOXYPHENYL)ETHYL 5-CHLORO-2,4-DIHYDROXYBENZOATE C₁₈ H₂₀ Cl N O₇ DFYGLJKFZQGYPA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.265 (Depositor), 0.276 (DCC)
R-Value Work: 0.230 (Depositor), 0.244 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.61	α = 90
b = 84.74	β = 90
c = 95.08	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Immormino, R.M.

Gewirth, D.T.

Revision History (Full details and data files)

Version 1.0: 2007-02-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-08-02
Changes: Source and taxonomy
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

2FYP | pdb_00002fyp

GRP94 in complex with the novel HSP90 Inhibitor Radester amine

Literature

Inhibittory Ligands Adopt Different Conformations When Bound to Hsp90 or GRP94: Implications for Paralog-specific Drug Design

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand