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6hhh

Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 31

Method: X-RAY DIFFRACTION Dmax: 69.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RAC-alpha serine/threonine-protein kinase

Homo sapiens

UniProt P31749

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–446 Not recorded G4Q ~{N}-[4-[4-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl)phenyl]methyl]piperazin-1-yl]phenyl]propanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 15% v/v PEG 2000 MME, pH 7.5, 3 mg/mL Akt1, (in 25 mM TRIS, 100 mM NaCl, 10 % Glycerol, 5 mM DTT, pH 7.5), 1ul reservoir + 1ul protein solution Resolution 2.70 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6HHH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1H10 HIGH RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF PROTEIN KINASE B/AKT BOUND TO INS(1,3,4,5)-TETRAKISPHOPHATE Deposited 2002-07-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–123（123 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-123
Non-standard monomer：Yes (specific site not provided by mmCIF) 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；0.25M AMMONIUM ACETATE, 30% PEG 4000,0.1M SODIUM ACETATE (PH 4.6)
Resolution 1.40 Å R-free 0.175
1UNP Crystal structure of the pleckstrin homology domain of PKB alpha Deposited 2003-09-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–121（121 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-121
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30 % PEG 4000, 0.25 M SODIUM ACETATE, 0.1 M TRIS PH 8.5 3.3 % POLYPROPYLENE GLYCOL 400
Resolution 1.65 Å R-free 0.236
1UNQ High resolution crystal structure of the Pleckstrin Homology Domain Of Protein Kinase B/Akt Bound To Ins(1,3,4,5)-Tetrakisphophate Deposited 2003-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–123（123 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN RESIDUES 1-123
Non-standard monomer：Yes (specific site not provided by mmCIF) 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.25 M AMMONIUM ACETATE, 30 % PEG 4000, 0.1 M SODIUM ACETATE (4.6), pH 4.60
Resolution 0.98 Å R-free 0.179
1UNR Crystal structure of the PH domain of PKB alpha in complex with a sulfate molecule Deposited 2003-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–123（123 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-123
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS (8.5) 0.2 M AMMONIUM SULFATE, pH 8.50
Resolution 1.25 Å R-free 0.226
2UVM Structure of PKBalpha PH domain in complex with a novel inositol headgroup surrogate, benzene 1,2,3,4-tetrakisphosphate Deposited 2007-03-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–123（123 aa） Fragment：PLECKSTRIN HOMOLOGY (PH) DOMAIN, RESIDUES 1-123
Not recorded GVF BENZENE-1,2,3,4-TETRAYL TETRAKIS[DIHYDROGEN (PHOSPHATE)] × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；25-30% POLYETHYLENE GLYCOL 3000, 0.1 M SODIUM ACETATE TRIHYDRATE [PH 4.4-5.0], 0.2 M AMMONIUM ACETATE
Resolution 1.94 Å R-free 0.269
2UZR A transforming mutation in the pleckstrin homology domain of AKT1 in cancer (AKT1-PH_E17K) Deposited 2007-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–123（123 aa） Fragment：RESIDUES 1-123
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；0.1 M HEPES PH 7.5 AND 1.4 M SODIUM CITRATE, OR 0.1 M SODIUM ACETATE PH 4.6, 0.2 M AMMONIUM ACETATE AND 15%-30% PEG 3350,
Resolution 1.94 Å R-free 0.257
2UZS A transforming mutation in the pleckstrin homology domain of AKT1 in cancer (AKT1-PH_E17K) Deposited 2007-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–123（123 aa） Fragment：RESIDUES 1-123
Mutation：E17K Non-standard monomer：Yes (specific site not provided by mmCIF) 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；GROWN FROM HANGING DROPS IN 0.1 M HEPES PH 7.5 AND 1.4 M SODIUM CITRATE, OR 0.1 M ACETATE PH 4.6, 0.2 M AMMONIUM ACETATE AND 15%-30% PEG 3350,
Resolution 2.46 Å R-free 0.286
3CQU Crystal Structure of Akt-1 complexed with substrate peptide and inhibitor Deposited 2008-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa） Fragment：Kinase and AGC-kinase C-terminal domains
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) CQU N-[2-(5-methyl-4H-1,2,4-triazol-3-yl)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.283
3CQW Crystal Structure of Akt-1 complexed with substrate peptide and inhibitor Deposited 2008-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa） Fragment：Kinase and AGC-kinase C-terminal domains
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 1 CQW 5-(5-chloro-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.257
3O96 Crystal Structure of Human AKT1 with an Allosteric Inhibitor Deposited 2010-08-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–443（442 aa） Fragment：unp residues 2-443
Not recorded IQO 1-(1-(4-(7-phenyl-1H-imidazo[4,5-g]quinoxalin-6-yl)benzyl)piperidin-4-yl)-1H-benzo[d]imidazol-2(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；50 mM acetate-citrate buffer, 21% PEG MME 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.308
3OW4 Discovery of dihydrothieno- and dihydrofuropyrimidines as potent pan Akt inhibitors Deposited 2010-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa）
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) SMY (2R)-3-(1H-indol-3-yl)-1-{4-[(5S)-5-methyl-5,7-dihydrothieno[3,4-d]pyrimidin-4-yl]piperazin-1-yl}-1-oxopropan-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Under oil；pH 7.5；293 K；8.3 mg/ml AKT1 protein, preincubated with 0.6 mM GSK3B peptide, 5 mM Mn-AMP-PNP. The precipitant was 20% PEG 4K, 15% isopropanol, 100 mM Hepes, pH 7.5, Under oil, temperature 293K
Resolution 2.60 Å R-free 0.268
3OW4 Discovery of dihydrothieno- and dihydrofuropyrimidines as potent pan Akt inhibitors Deposited 2010-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 144–480（337 aa）
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) SMY (2R)-3-(1H-indol-3-yl)-1-{4-[(5S)-5-methyl-5,7-dihydrothieno[3,4-d]pyrimidin-4-yl]piperazin-1-yl}-1-oxopropan-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Under oil；pH 7.5；293 K；8.3 mg/ml AKT1 protein, preincubated with 0.6 mM GSK3B peptide, 5 mM Mn-AMP-PNP. The precipitant was 20% PEG 4K, 15% isopropanol, 100 mM Hepes, pH 7.5, Under oil, temperature 293K
Resolution 2.60 Å R-free 0.268
3QKK Spirochromane Akt Inhibitors Deposited 2011-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa） Fragment：kinase domain
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) SMH N-(2-ethoxyethyl)-N-{(2S)-2-hydroxy-3-[(2R)-6-hydroxy-4-oxo-3,4-dihydro-1'H-spiro[chromene-2,3'-piperidin]-1'-yl]propyl}-2,6-dimethylbenzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Under oil；pH 7.8；293 K；8.1mg/ml protein, 0.6mM GSK-3 beta peptide, 5mM Mg-AMPPNP, 10mM DTT, 20% PEG 4K, 10% Isopropanol, 0.1M Hepes, pH 7.8, Under oil, temperature 293K
Resolution 2.30 Å R-free 0.250
3QKL Spirochromane Akt Inhibitors Deposited 2011-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa） Fragment：kinase domain
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) SMR N-{(2S)-3-[(3S)-8',9'-dihydro-1H,3'H-spiro[piperidine-3,7'-pyrano[3,2-e]indazol]-1-yl]-2-hydroxypropyl}-N-(2-ethoxyethyl)-2,6-dimethylbenzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Under oil；pH 7.8；293 K；9.7mg/ml protein, 0.6mM GSK-3 beta peptide, 1mM Mg-AMPPNP, 10mM DTT, 22% PEG 4K, 10% Isopropanol, 0.1M Hepes, pH 7.8, Under oil, temperature 293K
Resolution 1.90 Å R-free 0.243
3QKM Spirocyclic sulfonamides as AKT inhibitors Deposited 2011-02-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 144–480（337 aa） Fragment：kinase domain
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) SM9 N-(2-ethoxyethyl)-N-{(2S)-2-hydroxy-3-[(5R)-2-(quinazolin-4-yl)-2,7-diazaspiro[4.5]dec-7-yl]propyl}-2,6-dimethylbenzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Under oil；pH 7.8；293 K；9.7mg/ml protein, 0.6mM GSK-3 beta peptide, 1mM Mg-AMPPNP, 10mM DTT, 22% PEG 4K, 10% Isopropanol, 0.1M Hepes, pH 7.8, Under oil, temperature 293K
Resolution 2.20 Å R-free 0.252
4EJN Crystal structure of autoinhibited form of AKT1 in complex with N-(4-(5-(3-acetamidophenyl)-2-(2-aminopyridin-3-yl)-3H-imidazo[4,5-b]pyridin-3-yl)benzyl)-3-fluorobenzamide Deposited 2012-04-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Mutation：E114A, E115A, E116A 0R4 N-(4-{5-[3-(acetylamino)phenyl]-2-(2-aminopyridin-3-yl)-3H-imidazo[4,5-b]pyridin-3-yl}benzyl)-3-fluorobenzamide × 1 SBT 2-BUTANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；277 K；16% butanol, 10mM ammonium sulfate, 0.1% 2-mercaptoethanol, 15% ethylene glycol, 50mM Tris , pH 7.5, EVAPORATION, temperature 277K
Resolution 2.19 Å R-free 0.276
4EKK Akt1 with AMP-PNP Deposited 2012-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa） Fragment：UNP residues 144-480
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；20% PEG4K, 100mM Tris-pH7.5, Under Oil, temperature 293K
Resolution 2.80 Å R-free 0.280
4EKK Akt1 with AMP-PNP Deposited 2012-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 144–480（337 aa） Fragment：UNP residues 144-480
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；20% PEG4K, 100mM Tris-pH7.5, Under Oil, temperature 293K
Resolution 2.80 Å R-free 0.280
4EKL Akt1 with GDC0068 Deposited 2012-04-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 144–480（337 aa） Fragment：UNP residues 144-480
Mutation：S473D Non-standard monomer：Yes (specific site not provided by mmCIF) 0RF (2S)-2-(4-chlorophenyl)-1-{4-[(5R,7R)-7-hydroxy-5-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl]piperazin-1-yl}-3-(propan-2-ylamino)propan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Under Oil；pH 7.5；293 K；20% PEG4K 100mM Tris-pH7.5, Under Oil, temperature 293K
Resolution 2.00 Å R-free 0.235
4GV1 PKB alpha in complex with AZD5363 Deposited 2012-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 144–480（337 aa） Fragment：kinase domain (UNP residues 144-480)
Non-standard monomer：Yes (specific site not provided by mmCIF) 0XZ 4-amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；alcohol, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.49 Å R-free 0.210
5KCV Crystal structure of allosteric inhibitor, ARQ 092, in complex with autoinhibited form of AKT1 Deposited 2016-06-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Mutation：E114A, E115A, E116A 6S1 3-[3-[4-(1-azanylcyclobutyl)phenyl]-5-phenyl-imidazo[4,5-b]pyridin-2-yl]pyridin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；16% butanol, 10mM ammonium sulfate, 0.1% 2-mercaptoethanol, 15% ethylene glycol, 50mM Tris, pH 7.5
Resolution 2.70 Å R-free 0.269
6BUU Crystal structure of AKT1 (aa 144-480) with a bisubstrate Deposited 2017-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 144–480（337 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20% PEG 3000, 0.1M Hepes HCL, 0.2M Ammonium sulfate
Resolution 2.40 Å R-free 0.230
6BUU Crystal structure of AKT1 (aa 144-480) with a bisubstrate Deposited 2017-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 144–480（337 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20% PEG 3000, 0.1M Hepes HCL, 0.2M Ammonium sulfate
Resolution 2.40 Å R-free 0.230
6CCY Crystal structure of Akt1 in complex with a selective inhibitor Deposited 2018-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 144–466（323 aa）
Mutation：N199S, S396P, E397S, T433V Non-standard monomer：Yes (specific site not provided by mmCIF) EX4 (5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；16% PEG 3350 and 200mM Ammonium Formate
Resolution 2.18 Å R-free 0.276
6HHF Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor Borussertib Deposited 2018-08-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Not recorded G4K Borussertib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 15% v/v PEG 2000 MME, pH 5.2, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10 % Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Resolution 2.90 Å R-free 0.274
6HHG Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 27 Deposited 2018-08-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Not recorded G4T ~{N}-[2-chloranyl-5-[[1-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl)phenyl]methyl]piperidin-4-yl]carbamoylamino]phenyl]propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 15% v/v PEG 2000 MME, pH 7.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10 % Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Resolution 2.30 Å R-free 0.246
6HHI Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 30b Deposited 2018-08-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Not recorded G4N ~{N}-[1-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl)phenyl]methyl]piperidin-4-yl]-3-(propanoylamino)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 21% v/v PEG 2000 MME, pH 6.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10 % Glycerol, 5 mM DTT, pH 7.5), 1ul reservoir + 1ul protein solution
Resolution 2.70 Å R-free 0.258
6HHJ Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 24b Deposited 2018-08-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Not recorded G4H ~{N}-[1-methyl-2-oxidanylidene-3-[1-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl)phenyl]methyl]piperidin-4-yl]benzimidazol-5-yl]propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 15 % v/v PEG 2000 MME, pH 7.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10 % Glycerol, 5 mM DTT, pH 7.5), 1ul reservoir + 1ul protein solution
Resolution 2.30 Å R-free 0.243
6NPZ Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate Deposited 2019-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 123–480（358 aa） Fragment：UNP residues 123-480
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PGE TRIETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；12.5% PEG3350, 0.1 M HEPES-HCl, 0.2 M ammonium acetate
Resolution 2.12 Å R-free 0.241
6NPZ Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate Deposited 2019-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 123–480（358 aa） Fragment：UNP residues 123-480
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 VO4 VANADATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；12.5% PEG3350, 0.1 M HEPES-HCl, 0.2 M ammonium acetate
Resolution 2.12 Å R-free 0.241
6S9W Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 16a Deposited 2019-07-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Not recorded L1Z ~{N}-[3-[1-[[4-(5-methyl-6-oxidanylidene-3-phenyl-1~{H}-pyrazin-2-yl)phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 24% v/v PEG 2000 MME, pH 7.0, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10% v/v Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Resolution 2.30 Å R-free 0.263
6S9X Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 15c Deposited 2019-07-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Not recorded L1W ~{N}-[3-[1-[[4-[5-[(4-hydroxyphenyl)methyl]-6-oxidanylidene-2-phenyl-1~{H}-pyrazin-3-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 15% v/v PEG 2000 MME, pH 7.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10% v/v Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Resolution 2.60 Å R-free 0.234
7APJ Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation Deposited 2020-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–119（119 aa）
Chain A 134–445（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；200 mM malonate, pH 5.0, 16% PEG 3350
Resolution 2.05 Å R-free 0.252
7MYX Crystal structure of the PH domain (R86A) of Akt1 Deposited 2021-05-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–121（121 aa） Fragment：PH domain, UNP residues 1-121
Mutation：R86A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；1.28 M Sodium Citrate, 0.1 M Hepes pH 7.5, 0.01 M Praseodymium(III) Acetate
Resolution 1.39 Å R-free 0.204
7NH4 Co-Crystal Structure of Akt1 in Complex with Covalent-Allosteric Akt Inhibitor 3 Deposited 2021-02-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Mutation：E114A, E115A, E116A UCE ~{N}-[3-[1-[[4-[5-(hydroxymethyl)-3-phenyl-pyridin-2-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 12% v/v PEG 2000 MME, pH 6.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10% v/v Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Resolution 2.30 Å R-free 0.246
7NH5 Co-Crystal Structure of Akt1 in Complex with Covalent-Allosteric Akt Inhibitor 6 Deposited 2021-02-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–446（445 aa）
Mutation：E114A, E115A, E116A ACT ACETATE ION × 1 UC8 ~{N}-methyl-6-[4-[[4-[2-oxidanylidene-6-(propanoylamino)-3~{H}-benzimidazol-1-yl]piperidin-1-yl]methyl]phenyl]-5-phenyl-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.25 mM Na-acetate, 3.75 mM Na-citrate, 18% v/v PEG 2000 MME, pH 6.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10% v/v Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Resolution 1.90 Å R-free 0.228
8UVY Structure of AKT1(E17K) with compound 3 Deposited 2023-11-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–446（445 aa）
Mutation：E17K EDO 1,2-ETHANEDIOL × 1 XOO 4-{2-[({4-[(2P)-2-(2-aminopyridin-3-yl)-5-phenyl-3H-imidazo[4,5-b]pyridin-3-yl]phenyl}methyl)amino]ethyl}-2-hydroxybenzaldehyde × 1 SO4 SULFATE ION × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；29% PEG3350, 200 mM Li2SO4, 100 mM BisTris Propane pH 8.5, 10% ethylene glycol
Resolution 2.11 Å R-free 0.255
8UW2 Structure of AKT1(E17K) with compound 3 (zinc-free) Deposited 2023-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–446（445 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 XOO 4-{2-[({4-[(2P)-2-(2-aminopyridin-3-yl)-5-phenyl-3H-imidazo[4,5-b]pyridin-3-yl]phenyl}methyl)amino]ethyl}-2-hydroxybenzaldehyde × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；19% PEG3350, 200 mM Li2SO4, 100 mM BisTris Propane pH 8.5, 10% ethylene glycol
Resolution 2.20 Å R-free 0.279
8UW7 Structure of AKT1(WT) with compound 3 Deposited 2023-11-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–446（445 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 4 XOO 4-{2-[({4-[(2P)-2-(2-aminopyridin-3-yl)-5-phenyl-3H-imidazo[4,5-b]pyridin-3-yl]phenyl}methyl)amino]ethyl}-2-hydroxybenzaldehyde × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；19% PEG3350, 200 mM Na2SO4, 100 mM BisTris Propane pH 7.2, 10% ethylene glycol
Resolution 1.97 Å R-free 0.265
8UW9 Structure of AKT1(E17K) with compound 4 Deposited 2023-11-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–446（445 aa）
Not recorded XQ2 N-({4-[(2P)-2-(2-aminopyridin-3-yl)-5-phenyl-3H-imidazo[4,5-b]pyridin-3-yl]phenyl}methyl)-2-(2-fluoro-4-formyl-3-hydroxyphenyl)acetamide × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 4 ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG3350, 200 mM Li2SO4, 100 mM BisTris Propane pH 6.5, 10% ethylene glycol
Resolution 1.90 Å R-free 0.245
9ZBK mTORC2 in complex with Akt1 Deposited 2025-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 141–478（338 aa）
Not recorded ZN ZINC ION × 1 A1AID (1M,9M)-1-{4-[4-(prop-2-enoyl)piperazin-1-yl]-3-(trifluoromethyl)phenyl}-9-(quinolin-3-yl)benzo[h][1,6]naphthyridin-2(1H)-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å

37 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AKT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–446； UniProt 2–446

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6hhh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hhh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hhh
Deposition date deposition_date2018-08-28
Structure title titleCrystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 31
Keywords keywordsAkt1, covalent-allosteric, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.93 Å
Radius of gyration Rg (electron density) rg_electron21.60 Å
Forward intensity I(0) i032385100.00
Molecular weight molecular_weight44928.0 kDa
Excluded volume excluded_volume56758 ų
Envelope volume envelope_volume68447 ų
Hydration-shell volume shell_volume25911 ų
Envelope diameter envelope_diameter71.4 Å
Shell Rg shell_rg28.76 Å
Envelope Rg envelope_rg21.70 Å
Shape Rg shape_rg21.58 Å
Total Rg total_rg22.59 Å
Total atoms total_atoms3173
Residues n_residues379
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.3 Å
Rg (real space) rg_real22.80 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real3.2390e+07
I(0) uncertainty (real space) i0_real_error3.7700e+05
Rg (reciprocal space) rg_reciprocal22.84 Å
I(0) (reciprocal space) i0_reciprocal32390000.0000
Solution quality estimate total_estimate0.9107
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7 Å
Skewness Skewness skewness0.150
Kurtosis Kurtosis kurtosis-0.528
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8747000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6hhhA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id6hhhA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6hhhA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)