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- PDB-9s6m: Structure of BFL1 in complex with a covalent inhibitor, alternati... -

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Basic information

Entry
Database: PDB / ID: 9s6m
TitleStructure of BFL1 in complex with a covalent inhibitor, alternative series, cmpd25
ComponentsBcl-2-related protein A1
KeywordsAPOPTOSIS / BFL1 / Covalent / Inhibitor
Function / homology
Function and homology information


Regulation of MITF-M-dependent genes involved in apoptosis / mitochondrial fusion / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / mitochondrial outer membrane / positive regulation of apoptotic process / negative regulation of apoptotic process ...Regulation of MITF-M-dependent genes involved in apoptosis / mitochondrial fusion / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / mitochondrial outer membrane / positive regulation of apoptotic process / negative regulation of apoptotic process / cytosol / cytoplasm
Similarity search - Function
Bcl-2-related protein A1 / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family ...Bcl-2-related protein A1 / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
: / Bcl-2-related protein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.427 Å
AuthorsCottee, M.A. / Hargreaves, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: J.Med.Chem. / Year: 2026
Title: Optimization and Chemoproteomic Profiling of a Selective, Covalent Bfl-1-Targeting Cellular Tool.
Authors: Blackwell, J.H. / Lucas, S.C.C. / Battocchio, G. / Borjesson, U. / Bostock, M.J. / Braybrooke, E.L. / Cheung, T. / Cottee, M.A. / Beaumont, K.C. / Gohlke, A. / Hargreaves, D. / van Hoek- ...Authors: Blackwell, J.H. / Lucas, S.C.C. / Battocchio, G. / Borjesson, U. / Bostock, M.J. / Braybrooke, E.L. / Cheung, T. / Cottee, M.A. / Beaumont, K.C. / Gohlke, A. / Hargreaves, D. / van Hoek-Emmelot, M. / van Hoeven, V. / Jansen, C. / Kawatkar, A. / Kinzel, O. / Kumar, P. / Kupcova, L. / Lainchbury, M.D. / Leon, L. / Milbradt, A.G. / Palisse, A. / Schade, M. / van Rijbroek, K. / Sacchetto, C. / Schellekens, R. / Su, N. / Xu, H. / Zhao, H. / Chen, Y. / Huang, S.
History
DepositionAug 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-related protein A1
B: Bcl-2-related protein A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8134
Polymers34,8862
Non-polymers9272
Water2,828157
1
A: Bcl-2-related protein A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9062
Polymers17,4431
Non-polymers4631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bcl-2-related protein A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9062
Polymers17,4431
Non-polymers4631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.634, 43.382, 62.055
Angle α, β, γ (deg.)90, 93.63, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bcl-2-related protein A1 / Bcl-2-like protein 5 / Bcl2-L-5 / Hemopoietic-specific early response protein / Protein BFL-1 / Protein GRS


Mass: 17442.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2A1, BCL2L5, BFL1, GRS, HBPA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16548
#2: Chemical ChemComp-A1JL2 / (1~{R},2~{R})-2-azanyl-~{N}-[4-[(1~{R})-1-[propanoyl-[4-(trifluoromethyloxy)phenyl]amino]ethyl]phenyl]cyclopentane-1-carboxamide


Mass: 463.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: Typically grew as plates/pointed flat rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 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 ...Details: 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
PH range: 4.5-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.427→61.93 Å / Num. obs: 43147 / % possible obs: 76.9 % / Redundancy: 5 % / Biso Wilson estimate: 21.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Net I/σ(I): 12.8
Reflection shellResolution: 1.427→1.546 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2159 / CC1/2: 0.683 / Rpim(I) all: 0.407 / Rrim(I) all: 0.909 / % possible all: 18.2

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCautoPROC 1.0.5 (20220608)data reduction
XDSJan 10, 2022 (BUILT 20220110)data reduction
STARANISO2.3.87 (20220518)data scaling
Aimless0.7.9data scaling
PHASER2.8.3phasing
Coot0.9.8.93model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.427→61.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.085 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2219 -RANDOM
Rwork0.1943 ---
obs0.1954 43147 76.8 %-
Displacement parametersBiso mean: 24.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.1749 Å20 Å20.6613 Å2
2---0.4017 Å20 Å2
3---0.2268 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.427→61.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 66 157 2582
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112502HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983403HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d878SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes448HARMONIC5
X-RAY DIFFRACTIONt_it2502HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2484SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion16.47
LS refinement shellResolution: 1.43→1.51 Å
RfactorNum. reflection% reflection
Rfree0.2537 49 -
Rwork0.2601 --
obs0.2598 863 10.24 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8061-0.22730.04590.9467-0.27991.02970.03220.08280.00750.0828-0.00750.04230.00750.0423-0.0246-0.0872-0.01080.0091-0.0995-0.0103-0.090527.0658-0.305811.2059
21.67460.84790.051.61440.09420.7353-0.0617-0.1909-0.0138-0.19090.0736-0.0592-0.0138-0.0592-0.012-0.08830.00210.0126-0.08890.0082-0.09220.8094-21.678120.0869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 151
2X-RAY DIFFRACTION2{ B|* }B3 - 151

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