6s9w

Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 16a

Method: X-RAY DIFFRACTION D_max: 69.9 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

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	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

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 6S9W	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
6HHH Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 31 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	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
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
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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6s9w
Deposition date deposition_date	2019-07-15
Structure title title	Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 16a
Keywords keywords	Akt1, Akt2, Akt3, borussertib, covalent-allosteric, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.30 Å
Radius of gyration Rg (electron density) rg_electron	21.99 Å
Forward intensity I(0) i0	37968900.00
Molecular weight molecular_weight	48647.0 kDa
Excluded volume excluded_volume	61363 Å³
Envelope volume envelope_volume	74207 Å³
Hydration-shell volume shell_volume	27400 Å³
Envelope diameter envelope_diameter	72.0 Å
Shell Rg shell_rg	29.39 Å
Envelope Rg envelope_rg	22.07 Å
Shape Rg shape_rg	21.97 Å
Total Rg total_rg	22.96 Å
Total atoms total_atoms	3433
Residues n_residues	411
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	69.9 Å
Rg (real space) rg_real	23.14 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.7970e+07
I(0) uncertainty (real space) i0_real_error	4.3380e+05
Rg (reciprocal space) rg_reciprocal	23.18 Å
I(0) (reciprocal space) i0_reciprocal	37970000.0000
Solution quality estimate total_estimate	0.9112
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.119
Kurtosis Kurtosis kurtosis	-0.533
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12960000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RAC-alpha serine/threonine-protein kinase
Molecular weight formula_weight	51746.0 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3451

GSDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFSVAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQAAAEMDFRSGSPSDNSGAEEMEVSLAKPKHRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKDEVAHTLTENRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLSRERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQRLGGGSEDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSETDTRYFDEEFTAQM

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	;~{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 ;
Molecular weight formula_weight	562.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6s9wA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	6s9wA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	6s9wA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	70.070 Å
Unit-cell length b length_b	71.030 Å
Unit-cell length c length_c	91.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.670 Å
R factor r_factor	0.2099
R_work r_work	0.2071
R_free r_free	0.2625

fit	/app/data/saxs_computation/s9/6s9w/6s9w.fit
pddf	/app/data/pr_computation/s9/6s9w/6s9w.pr.out
profile	/app/data/saxs_computation/s9/6s9w/6s9w.dat