7Y8L | pdb_00007y8l

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

PDB DOI: https://doi.org/10.2210/pdb7Y8L/pdb

Classification: OXIDOREDUCTASE/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: 2.41 Å
R-Value Free:
0.265 (Depositor), 0.242 (DCC)
R-Value Work:
0.208 (Depositor), 0.226 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 125.8 kDa
Atom Count: 8,843
Modeled Residue Count: 1,145
Deposited Residue Count: 1,160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
reductase for protein	A, B, C, D	290	Streptomyces clavuligerus	Mutation(s): 0
UniProt
Find proteins for E2PUR9 (Streptomyces clavuligerus) Explore E2PUR9 Go to UniProtKB: E2PUR9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E2PUR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], L [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth D]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
4IS (Subject of Investigation/LOI) Query on 4IS Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], K [auth C]	5-[2,5-bis(fluoranyl)phenyl]-3,4-dihydro-2~{H}-pyrrole C₁₀ H₉ F₂ N QIZHVCUPPAMGIW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C]