7MU5 | pdb_00007mu5

Human DCTPP1 bound to Triptolide

PDB DOI: https://doi.org/10.2210/pdb7MU5/pdb

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

Deposited: 2021-05-14 Released: 2022-08-24
Deposition Author(s): Hauk, G., Berger, J.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.235 (Depositor), 0.238 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.186 (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

Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance

Liu, J., He, Q.-L., Zhou, J., Chikarmane, R.V., Hauk, G., Rachakonda, A., Vaghasia, A.M., Castagna, N., Steinberg, R.C., Anders, N.M., Wanjiku, T.M., Nuhn, P., Shim, J.S., Giovinazzo, H., Esopi, D.M., Kim, K., Coulter, J., Wang, R., Zhou, J., Rudek, M.A., Berger, J.M., Liu, J.O., Nelson, W.G., Yegnasubramanian, S.

To be published.

Macromolecule Content

Total Structure Weight: 104.52 kDa
Atom Count: 7,212
Modeled Residue Count: 843
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dCTP pyrophosphatase 1	A, B, C, D, E A, B, C, D, E, F, G, H	110	Homo sapiens	Mutation(s): 0 Gene Names: DCTPP1, XTP3TPA, CDA03 EC: 3.6.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H773 (Homo sapiens) Explore Q9H773 Go to UniProtKB: Q9H773
PHAROS: Q9H773 GTEx: ENSG00000179958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H773
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLI (Subject of Investigation/LOI) Query on TLI Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth F] SDF format, chain V [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G]	J [auth A] K [auth A] M [auth B] N [auth B] P [auth C] J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], Q [auth D], T [auth F], V [auth G]	triptolide C₂₀ H₂₄ O₆ DFBIRQPKNDILPW-CIVMWXNOSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain T [auth F] Focus chain V [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain T [auth F] Focus chain V [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G]	I [auth A] L [auth B] O [auth C] R [auth E] S [auth F] I [auth A], L [auth B], O [auth C], R [auth E], S [auth F], U [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth E] Focus chain S [auth F] Focus chain U [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth E] Focus chain S [auth F] Focus chain U [auth G]