9EZJ

Apo human TDO in complex with a bound inhibitor (Cpd-4)

PDB DOI: https://doi.org/10.2210/pdb9EZJ/pdb

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

Deposited: 2024-04-12 Released: 2024-06-05
Deposition Author(s): Wicki, M., Mac Sweeney, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.330
R-Value Work: 0.298
R-Value Observed: 0.299

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery and binding mode of small molecule inhibitors of the apo form of human TDO2

Lotz-Jenne, C., lange, R., Cren, S., Bourquin, G., Goglia, L., Kimmerlin, T., Wicki, M., Mueller, M., Artico, N., Ackerknecht, S., Joesch, C., Mac Sweeney, A.

To be published.

Macromolecule Content

Total Structure Weight: 193.99 kDa
Atom Count: 10,283
Modelled Residue Count: 1,260
Deposited Residue Count: 1,612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D	403	Homo sapiens	Mutation(s): 0 Gene Names: TDO2, TDO EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens) Explore P48775 Go to UniProtKB: P48775
PHAROS: P48775 GTEx: ENSG00000151790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48775
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H8G (Subject of Investigation/LOI) Query on A1H8G Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	ethyl (9~{R})-2-methoxy-4-oxidanylidene-9-[[(1~{S})-1-phenylethyl]-[(2-propan-2-ylphenyl)carbamoyl]amino]-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidine-3-carboxylate C₃₀ H₃₆ N₄ O₅ MLCVKHFILIDRCO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ZIQ Query on ZIQ Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	alpha-methyl-L-tryptophan C₁₂ H₁₄ N₂ O₂ ZTTWHZHBPDYSQB-LBPRGKRZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]