8CG9

Crystal structure of human DNA cross-link repair 1A in complex with a cyclic N-hydroxyurea inhibitor

PDB DOI: https://doi.org/10.2210/pdb8CG9/pdb

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

Deposited: 2023-02-03 Released: 2024-02-21
Deposition Author(s): Newman, J.A., Yosaatmadja, Y., Baddock, H.T., Bielinski, M., von Delft, F., Bountra, C., McHugh, P.J., Schofield, C.J., Gileadi, O.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.231
R-Value Work: 0.223
R-Value Observed: 0.223

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 human DNA cross-link repair 1A in complex with a cyclic N-hydroxyurea inhibitor

Newman, J.A., Yosaatmadja, Y., Baddock, H.T., Bielinski, M., von Delft, F., Bountra, C., McHugh, P.J., Schofield, C.J., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 40.03 kDa
Atom Count: 2,749
Modelled Residue Count: 331
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA cross-link repair 1A protein	A	345	Homo sapiens	Mutation(s): 0 Gene Names: DCLRE1A, KIAA0086, SNM1, SNM1A EC: 3.5.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PJP8 (Homo sapiens) Explore Q6PJP8 Go to UniProtKB: Q6PJP8
PHAROS: Q6PJP8 GTEx: ENSG00000198924
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PJP8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R3Z Query on R3Z Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione C₁₅ H₁₂ N₂ O₅ S MXQGCMQXTPTJJT-VIFPVBQESA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
XOB (Subject of Investigation/LOI) Query on XOB Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione C₁₅ H₁₂ N₂ O₅ S MXQGCMQXTPTJJT-SECBINFHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]