6S7H | pdb_00006s7h

Human CD73 (5'-nucleotidase) in complex with PSB12489 (an AOPCP derivative) in the closed state

• PDB DOI: https://doi.org/10.2210/pdb6S7H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-04 Released: 2020-07-22 
• Deposition Author(s): Pippel, J., Strater, N.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.199 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

X-Ray Co-Crystal Structure Guides the Way to Subnanomolar Competitive Ecto-5'-Nucleotidase (CD73) Inhibitors for Cancer Immunotherapy

Bhattarai, S., Pippel, J., Meyer, A., Freundlieb, M., Schmies, C., Abdelrahman, A., Fiene, A., Lee, S.Y., Zimmermann, H., El-Tayeb, A., Yegutkin, G.G., Strater, N., Muller, C.E.

(2019) Adv Ther 

• DOI: https://doi.org/10.1002/adtp.201900075

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.03 kDa 
• Atom Count: 4,441 
• Modeled Residue Count: 519 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-nucleotidase	A	532	Homo sapiens	Mutation(s): 4  Gene Names: NT5E, NT5, NTE EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt), 3.1.3.89 (UniProt), 3.1.3.35 (UniProt), 3.1.3.91 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21589 (Homo sapiens) Explore P21589  Go to UniProtKB:  P21589
PHAROS:  P21589 GTEx:  ENSG00000135318

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KYW (Subject of Investigation/LOI)	E [auth A]	(N6,N6)-methyl,benzyl-C2-chloro-(alpha,beta)-methylene-ADP C19 H24 Cl N5 O9 P2 NRCRRUYZIFHEBT-SCFUHWHPSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KYW	BindingDB:  6S7H	Ki: min: 0.32, max: 0.75 (nM) from 3 assay(s)
		IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.199 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.83	α = 90
b = 95.8	β = 90
c = 233.59	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Pippel, J., Strater, N.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	STR 477/13-2

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary