9fky

Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors

Method: X-RAY DIFFRACTION D_max: 79.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bcl-2-related protein A1

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 1–151	Not recorded	A1IDP ~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(1~{S})-1-[3-cyano-4-(trifluoromethyl)phenyl]ethyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；310 K；PCPT 0.1M pH 5, Na3 Cit 1.1M	Resolution 1.56 Å R-free 0.237
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–151	Not recorded	A1IDP ~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(1~{S})-1-[3-cyano-4-(trifluoromethyl)phenyl]ethyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；310 K；PCPT 0.1M pH 5, Na3 Cit 1.1M	Resolution 1.56 Å R-free 0.237

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 9FKY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VM6 Human Bcl2-A1 in complex with Bim-BH3 peptide Deposited 2008-01-23	Different construct 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 1–149（149 aa） Fragment：RESIDUES 1-149	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.1M BIS, TRIS PH 5.8, 2M AMSO4	Resolution 2.20 Å R-free 0.250
3I1H Crystal structure of human BFL-1 in complex with BAK BH3 peptide Deposited 2009-06-26	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 1–151（151 aa） Fragment：residues 1-151	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；1.5 M sodium malonate, pH 5.8 protein 1.67 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.238
3MQP Crystal Structure of human BFL-1 in complex with NOXA BH3 peptide, Northeast Structural Genomics Consortium Target HR2930 Deposited 2010-04-28	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 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；296 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 1.5 M Sodium Malonate, 0.1 M sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.24 Å R-free 0.230
4ZEQ Crystal Structure of human BFL-1 in complex with tBid BH3 peptide, Northeast Structural Genomics Consortium Target HX9247 Deposited 2015-04-20	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 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；Sodium Malonate	Resolution 1.80 Å R-free 0.239
5UUK Human Bfl-1 in complex with a Bfl-1-specific selected peptide Deposited 2017-02-17	Different construct 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 1–151（151 aa） Fragment：UNP residues 1-151	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 7.0	Resolution 1.20 Å R-free 0.163
5UUL Human Bfl-1 in complex with PUMA BH3 Deposited 2017-02-17	Different construct 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 1–151（151 aa） Fragment：UNP residues 1-151	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 7.0	Resolution 1.33 Å R-free 0.155
5UUP Human Bfl-1 covalently cross-linked to an electrophilic variant of a Bfl-1-specific selected peptide Deposited 2017-02-17	Different construct 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 1–151（151 aa） Fragment：UNP residues 1-151	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 7.0	Resolution 1.73 Å R-free 0.206
5WHH Crystal Structure of Bcl-2-related protein A1 in complex with stapled peptide (AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2) Deposited 2017-07-17	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 1–151（151 aa）	Mutation：C4S, C19S	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG3350 20%, 0.2M Sodium malonate	Resolution 2.38 Å R-free 0.293
5WHI Crystal Structure of Bcl-2-related protein A1 Deposited 2017-07-17	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 1–151（151 aa） Fragment：BFL1	Mutation：C4S, C19S	CAD CACODYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG2000	Resolution 1.69 Å R-free 0.233
6E3I Human Bfl-1 in complex with the Bfl-1-specific designed peptide srt.F4 Deposited 2018-07-14	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 1–151（151 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 7.0	Resolution 1.48 Å R-free 0.173
6E3J Human Bfl-1 in complex with the Bfl-1-specific designed peptide srt.F10 Deposited 2018-07-14	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 1–151（151 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 7.0	Resolution 1.48 Å R-free 0.178
6MBB Human Bfl-1 in complex with the designed peptide dF1 Deposited 2018-08-29	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 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 6.5	Resolution 1.59 Å R-free 0.196
6MBC Human Bfl-1 in complex with the designed peptide dF4 Deposited 2018-08-29	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 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；1.8 - 2.0 M NH4SO4, 50 mM MES pH 6.5	Resolution 1.75 Å R-free 0.212
6RJP Bfl-1 in complex with alpha helical peptide Deposited 2019-04-29	Different construct 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 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1 M sodium acetate pH 4.6 16% (w/v) PEG smear high	Resolution 2.57 Å R-free 0.266
6RJP Bfl-1 in complex with alpha helical peptide Deposited 2019-04-29	Different construct 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 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1 M sodium acetate pH 4.6 16% (w/v) PEG smear high	Resolution 2.57 Å R-free 0.266
6VO4 Crystal Structure Analysis of BFL1 Deposited 2020-01-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；3.5M Sodium formate, pH 7.0	Resolution 1.74 Å R-free 0.283
8RPO BFL1 in complex with a reversible covalent ligand Deposited 2024-01-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1H2C (~{E})-2-cyano-3-(2-dimethylphosphorylphenyl)-~{N}-[[1-[4-(trifluoromethyl)phenyl]cyclopropyl]methyl]prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；sodium citrate 0.3M, PCTP pH 6	Resolution 1.79 Å R-free 0.262
9EW8 Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors Deposited 2024-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1H7Q 1-[(2R)-2-phenylpyrrolidin-1-yl]propan-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.85M sodium citrate, 0.1M PCTP pH 6	Resolution 1.49 Å R-free 0.271
9FKZ Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors Deposited 2024-06-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1IDO ~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(4-chlorophenyl)methyl]prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；Na3 Cit 1M, PCPT 0.1M pH 7	Resolution 1.68 Å R-free 0.339
9FL0 Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors Deposited 2024-06-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1IDG ~{N}-[(4-chlorophenyl)methyl]-~{N}-(4-fluorophenyl)prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；PCPT 0.1M pH 7, Na3 Cit 1M	Resolution 1.94 Å R-free 0.281
9FL0 Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors Deposited 2024-06-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–151（151 aa）	Not recorded	A1IDG ~{N}-[(4-chlorophenyl)methyl]-~{N}-(4-fluorophenyl)prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；PCPT 0.1M pH 7, Na3 Cit 1M	Resolution 1.94 Å R-free 0.281
9GIP BFL1 covalently bound to inhibitor compound 7 Deposited 2024-08-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1ILY ~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(1~{S})-1-(4-chlorophenyl)ethyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.71；293 K；Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 8.71, Na3 Citrate 0.93 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.	Resolution 1.46 Å R-free 0.249
9GIQ BFL1 covalently bound to inhibitor compound 13 Deposited 2024-08-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	BUD (2S,3S)-butane-2,3-diol × 1 A1ILV ~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(1~{S})-1-(4-chlorophenyl)-3-methyl-3-oxidanyl-butyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 9.50, Na3 Citrate 0.60 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.	Resolution 1.42 Å R-free 0.257
9GIR BFL1 covalently bound to inhibitor compound 39 Deposited 2024-08-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1ILX ~{N}-[4-[(1~{R},3~{R})-3-[[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]carbamoylamino]cyclopentyl]oxy-3-chloranyl-phenyl]-~{N}-[(1~{S})-1-(4-chlorophenyl)ethyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.71；293 K；Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 4.78, Na3 Citrate 0.60 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.	Resolution 1.07 Å R-free 0.210
9GIS BFL1 covalently bound to inhibitor compound 17 Deposited 2024-08-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1ILU ~{N}-[(1~{S})-1-(4-chlorophenyl)ethyl]-~{N}-[4-[(1~{R},3~{R})-3-[[(3~{S})-pyrrolidin-3-yl]carbamoylamino]cyclopentyl]oxyphenyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.93；293 K；Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 7.93, Na3 Citrate 0.60 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.	Resolution 1.39 Å R-free 0.254
9GIS BFL1 covalently bound to inhibitor compound 17 Deposited 2024-08-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–151（151 aa）	Not recorded	A1ILU ~{N}-[(1~{S})-1-(4-chlorophenyl)ethyl]-~{N}-[4-[(1~{R},3~{R})-3-[[(3~{S})-pyrrolidin-3-yl]carbamoylamino]cyclopentyl]oxyphenyl]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.93；293 K；Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 7.93, Na3 Citrate 0.60 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.	Resolution 1.39 Å R-free 0.254
9GIT BFL1 covalently bound to inhibitor compound 43 Deposited 2024-08-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1ILW (3~{S})-3-[[4-[(1~{R},3~{R})-3-[[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]carbamoylamino]cyclopentyl]oxy-3-fluoranyl-phenyl]-propanoyl-amino]-3-(4-chlorophenyl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.14；293 K；Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 7.14, Na3 Citrate 0.92 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.	Resolution 1.15 Å R-free 0.212
9S6M Structure of BFL1 in complex with a covalent inhibitor, alternative series, cmpd25 Deposited 2025-08-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa）	Not recorded	A1JL2 (1~{R},2~{R})-2-azanyl-~{N}-[4-[(1~{R})-1-[propanoyl-[4-(trifluoromethyloxy)phenyl]amino]ethyl]phenyl]cyclopentane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization of adducted protein was carried out using a 2D optimization grid, (sodium citrate 0.6-1.1 M, vs PCTP buffer, 0.1 M pH 4.5-9.5). 300 nL drops (150 nL protein, 150 nL mother liquor) were incubated at 293 K in a sitting drop vapour diffusion format, dispensed using a Mosquito (SPT Labtech) and SWISSCI MRC 2-drop plates	Resolution 1.43 Å R-free 0.214
9S6M Structure of BFL1 in complex with a covalent inhibitor, alternative series, cmpd25 Deposited 2025-08-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–151（151 aa）	Not recorded	A1JL2 (1~{R},2~{R})-2-azanyl-~{N}-[4-[(1~{R})-1-[propanoyl-[4-(trifluoromethyloxy)phenyl]amino]ethyl]phenyl]cyclopentane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization of adducted protein was carried out using a 2D optimization grid, (sodium citrate 0.6-1.1 M, vs PCTP buffer, 0.1 M pH 4.5-9.5). 300 nL drops (150 nL protein, 150 nL mother liquor) were incubated at 293 K in a sitting drop vapour diffusion format, dispensed using a Mosquito (SPT Labtech) and SWISSCI MRC 2-drop plates	Resolution 1.43 Å R-free 0.214

25 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B2LA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–152； UniProt 1–151 Author chain B； PDBConstruct 2–152； UniProt 1–151

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	9fky
Deposition date deposition_date	2024-06-04
Structure title title	Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors
Keywords keywords	Bfl-1, Bcl-2-related protein A1, covalent, APOPTOSIS; APOPTOSIS
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	23.91 Å
Radius of gyration Rg (electron density) rg_electron	23.23 Å
Forward intensity I(0) i0	19097100.00
Molecular weight molecular_weight	34692.0 kDa
Excluded volume excluded_volume	43994 Å³
Envelope volume envelope_volume	53598 Å³
Hydration-shell volume shell_volume	20104 Å³
Envelope diameter envelope_diameter	80.2 Å
Shell Rg shell_rg	29.09 Å
Envelope Rg envelope_rg	23.32 Å
Shape Rg shape_rg	23.17 Å
Total Rg total_rg	24.21 Å
Total atoms total_atoms	2452
Residues n_residues	294
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	79.2 Å
Rg (real space) rg_real	24.02 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.9100e+07
I(0) uncertainty (real space) i0_real_error	2.7620e+05
Rg (reciprocal space) rg_reciprocal	24.00 Å
I(0) (reciprocal space) i0_reciprocal	19100000.0000
Solution quality estimate total_estimate	0.8682
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.455
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6432000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.970

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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	Bcl-2-related protein A1
Molecular weight formula_weight	17442.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2566

GMTDCEFGYIYRLAQDYLQCVLQIPQPGSGPSKTSRVLQNVAFSVQKEVEKNLKSCLDNVNVVSVDTARTLFNQVMEKEFEDGIINWGRIVTIFAFEGILIKKLLRQQIAPDVDTYKEISYFVAEFIMNNTGEWIRQNGGWENGFVKKFEPK

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	Escherichia

Entity 2 Entity 2 non-polymer

Description description	~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(1~{S})-1-[3-cyano-4-(trifluoromethyl)phenyl]ethyl]propanamide
Molecular weight formula_weight	445.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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8. Citations (1)

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Unit-cell length a length_a	56.927 Å
Unit-cell length b length_b	43.200 Å
Unit-cell length c length_c	62.088 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.557 Å
Low-resolution limit resolution_low	61.960 Å
R factor r_factor	0.2111
R_work r_work	0.2097
R_free r_free	0.2371

fit	/app/data/saxs_computation/fk/9fky/9fky.fit
pddf	/app/data/pr_computation/fk/9fky/9fky.pr.out
profile	/app/data/saxs_computation/fk/9fky/9fky.dat