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- PDB-9z3v: Histidine-covalent 165G1 targeting hMcl-1 -

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Basic information

Entry
Database: PDB / ID: 9z3v
TitleHistidine-covalent 165G1 targeting hMcl-1
Components
  • 165G1
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / Histidine-covalent stapled alpha-helical peptides
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / Bcl-2 family protein complex / mitochondrial fusion / negative regulation of anoikis / BH3 domain binding / transmembrane protein transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / Bcl-2 family protein complex / mitochondrial fusion / negative regulation of anoikis / BH3 domain binding / transmembrane protein transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / release of cytochrome c from mitochondria / negative regulation of autophagy / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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 ...Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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
Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlboreggia, G. / Atienza, E. / Muzzarelli, K.M. / Assar, Z. / Pellecchia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Covalent Targeting of Histidine Residues: A Ligand-First Approach.
Authors: Alboreggia, G. / Atienza, E.L. / Muzzarelli, K. / Assar, Z. / Pellecchia, M.
History
DepositionNov 7, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2026ID: 9CKN
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
C: 165G1
B: Induced myeloid leukemia cell differentiation protein Mcl-1
D: 165G1


Theoretical massNumber of molelcules
Total (without water)38,7304
Polymers38,7304
Non-polymers00
Water4,738263
1
A: Induced myeloid leukemia cell differentiation protein Mcl-1
C: 165G1


Theoretical massNumber of molelcules
Total (without water)19,3652
Polymers19,3652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area8260 Å2
MethodPISA
2
B: Induced myeloid leukemia cell differentiation protein Mcl-1
D: 165G1


Theoretical massNumber of molelcules
Total (without water)19,3652
Polymers19,3652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-8 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.514, 78.046, 62.254
Angle α, β, γ (deg.)90.000, 93.080, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17793.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Protein/peptide 165G1


Mass: 1571.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate: HCl, pH 4.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→48.62 Å / Num. obs: 276140 / % possible obs: 99.96 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.49
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 3987 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
autoPROC1.20.1_4487data processing
xia21.20.1_4487data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.62 Å / SU ML: 0.2421 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.0172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 1630 4.11 %
Rwork0.2245 38072 -
obs0.226 39702 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 34 263 2860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332633
X-RAY DIFFRACTIONf_angle_d0.59753527
X-RAY DIFFRACTIONf_chiral_restr0.0372389
X-RAY DIFFRACTIONf_plane_restr0.0049451
X-RAY DIFFRACTIONf_dihedral_angle_d14.6868985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.32671170.31013208X-RAY DIFFRACTION99.88
1.65-1.70.31911320.29473140X-RAY DIFFRACTION99.97
1.7-1.760.29531300.2773193X-RAY DIFFRACTION100
1.76-1.830.35061390.2843138X-RAY DIFFRACTION99.91
1.83-1.910.30711180.28853172X-RAY DIFFRACTION100
1.91-2.020.27381300.25773150X-RAY DIFFRACTION99.97
2.02-2.140.28521350.24383167X-RAY DIFFRACTION99.97
2.14-2.310.26931490.23183175X-RAY DIFFRACTION100
2.31-2.540.24171230.22863173X-RAY DIFFRACTION100
2.54-2.910.24181550.22453167X-RAY DIFFRACTION99.97
2.91-3.660.2961410.20853177X-RAY DIFFRACTION100
3.66-48.620.21541610.18783212X-RAY DIFFRACTION99.91

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