9FRM | pdb_00009frm

The crystal structure of glycogen phosphorylase with an indole derivative

PDB DOI: https://doi.org/10.2210/pdb9FRM/pdb

Classification: TRANSFERASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2024-06-19 Released: 2025-05-07
Deposition Author(s): Koulas, S.M., Leonidas, D.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Synthesis and evaluation of tetrahydrobenzo[cd]indole derivatives as glycogen phosphorylase inhibitors

Arunrattiyakorn, P., Juiprasert, C., Koulas, S.M., Boonsri, P., Aree, T., Yagi-Utsumi, M., Kato, K., Leonidas, D.D.

(2025) Med Chem Res

DOI: https://doi.org/10.1007/s00044-025-03384-7

Macromolecule Content

Total Structure Weight: 99.46 kDa
Atom Count: 7,241
Modeled Residue Count: 805
Deposited Residue Count: 843
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	843	Oryctolagus cuniculus	Mutation(s): 0 EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489 Go to UniProtKB: P00489
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IFQ (Subject of Investigation/LOI) Query on A1IFQ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(7~{S})-1-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)amino]-6,6-dimethyl-7-oxidanyl-7,8-dihydrobenzo[cd]indole-3-carboxylic acid C₂₆ H₂₄ N₂ O₅ UPILIIDBNLOCIT-NRFANRHFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS