7BN8 | pdb_00007bn8

Notum fragment_3 (4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid)

• PDB DOI: https://doi.org/10.2210/pdb7BN8/pdb

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


• Deposited: 2021-01-21 Released: 2022-03-02 
• Deposition Author(s): Zhao, Y., Jones, E.Y.
• Funding Organization(s): Cancer Research UK

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Notum Inhibitor

Zhao, Y., Jones, E.Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.4 kDa 
• Atom Count: 2,852 
• Modeled Residue Count: 348 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Palmitoleoyl-protein carboxylesterase NOTUM	A	383	Homo sapiens	Mutation(s): 1  Gene Names: NOTUM, OK/SW-CL.30 EC: 3.1.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P988 (Homo sapiens) Explore Q6P988  Go to UniProtKB:  Q6P988
PHAROS:  Q6P988 GTEx:  ENSG00000185269
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q6P988-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U4T (Subject of Investigation/LOI)	G [auth A]	4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid C13 H10 O2 S IGBRCZHGFVMFCR-UHFFFAOYSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
U4T	BindingDB:  7BN8	EC50: min: 361, max: 1060 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.44	α = 90
b = 72.426	β = 90
c = 79.347	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Zhao, Y., Jones, E.Y.

---

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C375/A17721

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary