6W4R | pdb_00006w4r

Structure of Tdp1 catalytic domain in complex with inhibitor XZ633p

PDB DOI: https://doi.org/10.2210/pdb6W4R/pdb

Classification: DNA BINDING PROTEIN, HYDROLASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-11 Released: 2021-03-17
Deposition Author(s): Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Pommier, Y., Burke, T.R., Waugh, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (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

Tdp1 catalytic domain

Lountos, G.T., Waugh, D.S.

To be published.

Macromolecule Content

Total Structure Weight: 105.55 kDa
Atom Count: 8,007
Modeled Residue Count: 876
Deposited Residue Count: 922
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 1	A, B	461	Homo sapiens	Mutation(s): 0 Gene Names: TDP1 EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUW8 (Homo sapiens) Explore Q9NUW8 Go to UniProtKB: Q9NUW8
PHAROS: Q9NUW8 GTEx: ENSG00000042088
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SZV (Subject of Investigation/LOI) Query on SZV Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	4-{[2-(2-hydroxyphenyl)imidazo[1,2-a]pyrazin-3-yl]amino}benzene-1,2-dicarboxylic acid C₂₀ H₁₄ N₄ O₅ XBODYKBLJPPTJV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MPO Query on MPO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]