7RRD | pdb_00007rrd

IDO1 IN COMPLEX WITH COMPOUND S-1

PDB DOI: https://doi.org/10.2210/pdb7RRD/pdb

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

Deposited: 2021-08-09 Released: 2022-08-24
Deposition Author(s): Lesburg, C.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.261 (Depositor), 0.208 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.215 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Oxetane promise delivered: discovery of long acting IDO1 inhibitors suitable for Q3W oral or parenteral dosing

Li, D., Sloman, D., Achab, A., Zhou, H., McGowan, M., White, C., Gibeau, C., Zhang, H., Pu, Q., Bharathan, I., Hopkins, B., Liu, K., Ferguson, H., Fradera, X., Lesburg, C.A., Martinot, T.A., Qi, J., Song, Z.J., Yin, J., Song, L., Wan, B., D'Addio, S., Solban, N., Miller, R., Zamlynny, B., Bass, A., Freeland, E., Ykoruk, B., Hilliard, C., Ferraro, J., Zhai, J., Knemayer, I., Otte, K., Vincent, S., Sciammetta, N., Pasternak, A., Bennett, D.J., Han, Y.

To be published.

Macromolecule Content

Total Structure Weight: 89.49 kDa
Atom Count: 6,045
Modeled Residue Count: 748
Deposited Residue Count: 788
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A, B	394	Homo sapiens	Mutation(s): 0 Gene Names: IDO1, IDO, INDO EC: 1.13.11.52
UniProt & NIH Common Fund Data Resources
Find proteins for P14902 (Homo sapiens) Explore P14902 Go to UniProtKB: P14902
PHAROS: P14902 GTEx: ENSG00000131203
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6IZ (Subject of Investigation/LOI) Query on 6IZ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	3-[4-(1H-benzimidazol-2-yl)phenyl]-N-(4-fluorophenyl)oxetane-3-carboxamide C₂₃ H₁₈ F N₃ O₂ OLDGOAIEJVEZFL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.261 (Depositor), 0.208 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.895	α = 90
b = 95.125	β = 90
c = 129.325	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary

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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.