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

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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 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X5T (Subject of Investigation/LOI)	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

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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Rangel, V., Zebisch, M., Doyle, K.J., Burli, R.W.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Database references