9EJQ | pdb_00009ejq

Crystal structure of DDB1 in complex with XS381952

PDB DOI: https://doi.org/10.2210/pdb9EJQ/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-11-28 Released: 2025-02-26
Deposition Author(s): Zeng, H., Ahmad, H., Wang, X., Sun, J., Dong, A., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Peng, H., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.161 (Depositor), 0.175 (DCC)
R-Value Observed:
0.164 (Depositor)

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

Crystal structure of DDB1 in complex with XS381952

Zeng, H., Ahmad, H., Wang, X., Sun, J., Dong, A., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Peng, H., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 129.48 kDa
Atom Count: 9,508
Modeled Residue Count: 1,119
Deposited Residue Count: 1,142
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	1,142	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531 GTEx: ENSG00000167986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BIX (Subject of Investigation/LOI) Query on A1BIX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(4S)-4-(3-ethoxyphenyl)-3-methyl-1-[(4R)-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one C₂₀ H₁₉ N₇ O₂ CAXXQNPHWIAQRY-HNNXBMFYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	P [auth A] Q [auth A] R [auth A] S [auth A] T [auth A] P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A]	D [auth A] E [auth A] K [auth A] L [auth A] M [auth A] D [auth A], E [auth A], K [auth A], L [auth A], M [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]