7Y8M

Structure of ScIRED-R2-V3 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole

• PDB DOI: https://doi.org/10.2210/pdb7Y8M/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Streptomyces clavuligerus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-24 Released: 2023-06-28 
• Deposition Author(s): Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.235 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Engineered Imine Reductase for Larotrectinib Intermediate Manufacture

Chen, Q., Li, B.B., Zhang, L., Chen, X.R., Zhu, X.X., Chen, F.F., Shi, M., Chen, C.C., Yang, Y., Guo, R.T., Liu, W., Xu, J.H., Zheng, G.W.

(2022) ACS Catal 12: 14795-14803

• DOI: https://doi.org/10.1021/acscatal.2c03783

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 125.81 kDa 
• Atom Count: 9,220 
• Modelled Residue Count: 1,149 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
reductase	A, B, C, D	290	Streptomyces clavuligerus	Mutation(s): 0
UniProt
Find proteins for E2PUR9 (Streptomyces clavuligerus) Explore E2PUR9  Go to UniProtKB:  E2PUR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	E [auth A], H [auth B], I [auth C], K [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
Q0R (Subject of Investigation/LOI)	F [auth A], G [auth A], J [auth C], L [auth D]	2-[2,5-bis(fluoranyl)phenyl]pyrrolidine C10 H11 F2 N NCXSNNVYILYEBC-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.235 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.456	α = 90
b = 67.668	β = 104.87
c = 140.764	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description