251,806
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

4CFF | pdb_00004cff

Structure of full length human AMPK in complex with a small molecule activator, a thienopyridone derivative (A-769662)

PDB DOI: https://doi.org/10.2210/pdb4CFF/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-11-14 Released: 2013-12-25
Deposition Author(s): Xiao, B., Sanders, M.J., Carmena, D., Bright, N.J., Haire, L.F., Underwood, E., Patel, B.R., Heath, R.B., Walker, P.A., Hallen, S., Giordanetto, F., Martin, S.R., Carling, D., Gamblin, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.92 Å
R-Value Free:
0.264 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural Basis of Ampk Regulation by Small Molecule Activators.

Xiao, B., Sanders, M.J., Carmena, D., Bright, N.J., Haire, L.F., Underwood, E., Patel, B.R., Heath, R.B., Walker, P.A., Hallen, S., Giordanetto, F., Martin, S.R., Carling, D., Gamblin, S.J.

(2013) Nat Commun 4: 3017

PubMed: 24352254 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ncomms4017
Primary Citation Related Structures:
4CFE, 4CFF

PubMed Abstract:
AMP-activated protein kinase (AMPK) plays a major role in regulating cellular energy balance by sensing and responding to increases in AMP/ADP concentration relative to ATP. Binding of AMP causes allosteric activation of the enzyme and binding of either AMP or ADP promotes and maintains the phosphorylation of threonine 172 within the activation loop of the kinase. AMPK has attracted widespread interest as a potential therapeutic target for metabolic diseases including type 2 diabetes and, more recently, cancer. A number of direct AMPK activators have been reported as having beneficial effects in treating metabolic diseases, but there has been no structural basis for activator binding to AMPK. Here we present the crystal structure of human AMPK in complex with a small molecule activator that binds at a site between the kinase domain and the carbohydrate-binding module, stabilising the interaction between these two components. The nature of the activator-binding pocket suggests the involvement of an additional, as yet unidentified, metabolite in the physiological regulation of AMPK. Importantly, the structure offers new opportunities for the design of small molecule activators of AMPK for treatment of metabolic disorders.

Organizational Affiliation

1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2].

1] MRC Clinical Sciences Centre, Cellular Stress Group, Hammersmith Hospital Campus, Imperial College, DuCane Road, London W12 0NN, UK [2].

MRC Clinical Sciences Centre, Cellular Stress Group, Hammersmith Hospital Campus, Imperial College, DuCane Road, London W12 0NN, UK.

MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

Bioscience, CVMD Innovative Medicine Unit, AstraZeneca R&D, Pepparedsleden 1, Mölndal S-43183, Sweden.

1] Medicinal Chemistry, CVMD Innovative Medicine Unit, AstraZeneca R&D, Pepparedsleden 1, Mölndal S-43183, Sweden [2].

Macromolecule Content

Total Structure Weight: 272.49 kDa
Atom Count: 14,484
Modeled Residue Count: 1,782
Deposited Residue Count: 2,376
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2	A, C	571	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data)	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P54646 (Homo sapiens) Explore P54646 Go to UniProtKB: P54646
PHAROS: P54646 GTEx: ENSG00000162409
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54646
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1	B, D	286	Homo sapiens	Mutation(s): 0	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens) Explore Q9Y478 Go to UniProtKB: Q9Y478
PHAROS: Q9Y478 GTEx: ENSG00000111725
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y478
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1	E, F	331	Homo sapiens	Mutation(s): 0	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens) Explore P54619 Go to UniProtKB: P54619
PHAROS: P54619 GTEx: ENSG00000181929
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54619
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STU Query on STU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C]	G [auth A], I [auth C]	STAUROSPORINE C₂₈ H₂₆ N₄ O₃ HKSZLNNOFSGOKW-FYTWVXJKSA-N	👁 Image	Focus chain G [auth A] Focus chain I [auth C] Focus chain G [auth A] Focus chain I [auth C]
C1V Query on C1V Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	H [auth B], J [auth C]	3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile C₂₀ H₁₂ N₂ O₃ S CTESJDQKVOEUOY-UHFFFAOYSA-N	👁 Image	Focus chain H [auth B] Focus chain J [auth C] Focus chain H [auth B] Focus chain J [auth C]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain M [auth F] SDF format, chain N [auth F] SDF format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] MOL2 format, chain K [auth E] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F] mmCIF format, chain K [auth E]	K [auth E], L [auth E], M [auth F], N [auth F]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N	👁 Image	Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth F] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A, C	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P	👁 Image	THR
SEP Query on SEP	B, D	L-PEPTIDE LINKING	C₃ H₈ N O₆ P	👁 Image	SER

Binding Affinity Annotations
ID	Source	Binding Affinity
C1V	BindingDB: 4CFF	Kd: min: 487, max: 1.45e+4 (nM) from 3 assay(s)
C1V	BindingDB: 4CFF	EC50: min: 390, max: 800 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.92 Å
R-Value Free: 0.264 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.019	α = 90
b = 134.787	β = 93.04
c = 141.286	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2014-01-08
Changes: Database references
Version 1.2: 2014-02-12
Changes: Data collection, Other, Refinement description
Version 1.3: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

URL: https://www.rcsb.org/structure/4CFF

⇱ RCSB PDB - 4CFF: Structure of full length human AMPK in complex with a small molecule activator, a thienopyridone derivative (A-769662)

4CFF | pdb_00004cff

Structure of full length human AMPK in complex with a small molecule activator, a thienopyridone derivative (A-769662)

Structural Basis of Ampk Regulation by Small Molecule Activators.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)