8P8C

HUMAN CD38 ECTODOMAIN BOUND TO COMPOUND 9-ADPR ADDUCT

PDB DOI: https://doi.org/10.2210/pdb8P8C/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2023-05-31 Released: 2023-07-26
Deposition Author(s): Rangel, V., Zebisch, M., Doyle, K.J., Burli, R.W.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.244
R-Value Work: 0.202
R-Value Observed: 0.204

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A Covalent Binding Mode of a Pyrazole-Based CD38 Inhibitor

Doyle, K., Roberts, M., Harvey, J., Hewer, R., Zebisch, M., Rangel, V., Gu, M., Wu, Y., Yang, L., Carlton, M., Dawson, L., Burli, R.

(2023) Helv Chim Acta 106

DOI: https://doi.org/10.1002/hlca.202300080

Macromolecule Content

Total Structure Weight: 30.61 kDa
Atom Count: 2,212
Modelled Residue Count: 241
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	A	256	Homo sapiens	Mutation(s): 4 Gene Names: CD38 EC: 3.2.2 (PDB Primary Data), 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens) Explore P28907 Go to UniProtKB: P28907
PHAROS: P28907 GTEx: ENSG00000004468
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28907
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X5T (Subject of Investigation/LOI) Query on X5T Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-[4-[[4-(2-methoxyethoxy)cyclohexyl]amino]-1-methyl-2-oxidanylidene-quinolin-6-yl]pyrazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C₃₇ H₄₉ N₉ O₁₆ P₂ WTFSRMVUMGMJHZ-YDMLZLAJSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.244
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.009	α = 90
b = 61.464	β = 90
c = 73.407	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2023-07-26
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Database references
Version 1.2: 2024-10-16
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.