2ZB2

Human liver glycogen phosphorylase a complexed with glcose and 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.300 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Synthesis of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives as inhibitors of human liver glycogen phosphorylase a.

Onda, K., Suzuki, T., Shiraki, R., Yonetoku, Y., Negoro, K., Momose, K., Katayama, N., Orita, M., Yamaguchi, T., Ohta, M., Tsukamoto, S.

(2008) Bioorg Med Chem 16: 5452-5464

  • DOI: 10.1016/j.bmc.2008.04.010
  • Primary Citation of Related Structures:  
    2ZB2

  • PubMed Abstract: 

    • A series of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives were prepared and evaluated as inhibitors of human liver glycogen phosphorylase a (hLGPa). One compound, 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide (2f), inhibited hLGPa with an IC(50) of 0 ...

    A series of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives were prepared and evaluated as inhibitors of human liver glycogen phosphorylase a (hLGPa). One compound, 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide (2f), inhibited hLGPa with an IC(50) of 0.90microM. The pyridine analogue of 2f showed inhibitory activity of glucagon-induced glucose output in cultured primary hepatocytes with an IC(50) of 0.62microM and oral hypoglycemic activity in diabetic db/db mice. Crystallographic determination of the complex of 2f with hLGPa showed binding of the inhibitor in a solvent cavity at the dimer interface, with the two hydroxyl groups making favorable electrostatic interactions with hLGPa.

    Organizational Affiliation: 

    Drug Discovery Research, Astellas Pharma Inc., 5-2-3 Toukoudai, Tsukuba, Ibaraki 300-2698, Japan. kenichi.onda@jp.astellas.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, liver formA, B849Homo sapiensMutation(s): 0 
Gene Names: PYGL
EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens)
Explore P06737 
Go to UniProtKB:  P06737
PHAROS:  P06737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06737
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A46
Query on A46
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]		5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide
C17 H15 Cl N2 O3
SHCHFGSUYJUEBR-INIZCTEOSA-N		 Ligand Interaction
PLP
Query on PLP
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GLC
Query on GLC
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
A46 BindingDB:  2ZB2 IC50: 900 (nM) from 1 assay(s)
Binding MOAD:  2ZB2 IC50: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.300 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.819α = 90
b = 123.819β = 90
c = 123.538γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNXphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary