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- PDB-7l26: HPK1 IN COMPLEX WITH COMPOUND 38 -

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Basic information

Entry
Database: PDB / ID: 7l26
TitleHPK1 IN COMPLEX WITH COMPOUND 38
ComponentsMitogen-activated protein kinase kinase kinase kinase 1
KeywordsTRANSFERASE / HPK1 HEMATOPOIETIC PROGENITOR KINASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-XHM / Mitogen-activated protein kinase kinase kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLesburg, C.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Identification of Potent Reverse Indazole Inhibitors for HPK1.
Authors: Yu, E.C. / Methot, J.L. / Fradera, X. / Lesburg, C.A. / Lacey, B.M. / Siliphaivanh, P. / Liu, P. / Smith, D.M. / Xu, Z. / Piesvaux, J.A. / Kawamura, S. / Xu, H. / Miller, J.R. / Bittinger, M. / Pasternak, A.
History
DepositionDec 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase kinase 1
B: Mitogen-activated protein kinase kinase kinase kinase 1
C: Mitogen-activated protein kinase kinase kinase kinase 1
D: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5848
Polymers128,8824
Non-polymers1,7024
Water4,143230
1
A: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6462
Polymers32,2211
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6462
Polymers32,2211
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6462
Polymers32,2211
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6462
Polymers32,2211
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.138, 58.168, 98.955
Angle α, β, γ (deg.)89.840, 90.130, 97.600
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 8 - 294 / Label seq-ID: 1 - 287

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Mitogen-activated protein kinase kinase kinase kinase 1 / Hematopoietic progenitor kinase / MAPK/ERK kinase kinase kinase 1 / MEKKK 1


Mass: 32220.621 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K1, HPK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92918, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-XHM / 6-(2-fluoro-6-methylphenyl)-1-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-5-carbonitrile


Mass: 425.501 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H24FN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: UNDISCLOSED

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.3→98.95 Å / Num. obs: 54548 / % possible obs: 95 % / Redundancy: 2.2 % / Biso Wilson estimate: 47.283 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.092 / Rsym value: 0.069 / Χ2: 0.975 / Net I/σ(I): 8.65
Reflection shellResolution: 2.3→2.55 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.56 / Num. unique obs: 14634 / CC1/2: 0.998 / Rrim(I) all: 0.568 / Rsym value: 0.435 / % possible all: 95.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED STUCTURE

Resolution: 2.3→98.95 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 29.626 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.436 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 1155 2.1 %RANDOM
Rwork0.2619 ---
obs0.2627 53146 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.05 Å2 / Biso mean: 64.411 Å2 / Biso min: 26.72 Å2
Baniso -1Baniso -2Baniso -3
1-4.47 Å2-0.43 Å21.81 Å2
2---0.3 Å2-3.3 Å2
3----4.07 Å2
Refinement stepCycle: final / Resolution: 2.3→98.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8790 0 128 230 9148
Biso mean--75.75 48.44 -
Num. residues----1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198833
X-RAY DIFFRACTIONr_bond_other_d0.0040.028484
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.98611998
X-RAY DIFFRACTIONr_angle_other_deg1.262319392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17251106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44623.871341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93615.0821470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7681538
X-RAY DIFFRACTIONr_chiral_restr0.0950.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219891
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021967
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A63540.01
12B63540.01
21A66940.01
22C66940.01
31A64080.02
32D64080.02
41B63260.01
42C63260.01
51B63960.01
52D63960.01
61C63580.02
62D63580.02
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 73 -
Rwork0.382 3950 -
all-4023 -
obs--94.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.7061-2.12294.41037.6825-8.336112.34070.4507-0.14290.0066-0.6721-0.20610.09150.4781-0.3929-0.24470.8564-0.4408-0.14750.94390.14740.4058-6.75.045-61.417
22.8968-1.21591.41077.966-6.96159.9763-0.0743-0.821-0.28131.40910.11430.4832-1.1165-0.518-0.03990.5699-0.3242-0.16370.57760.22870.341916.3812.968-67.987
33.27571.2769-1.11823.3278-0.48063.3037-0.12730.0563-0.0655-0.15390.04350.02810.29110.14460.08380.4138-0.3964-0.22450.44190.24690.141712.1255.218-42.289
45.7691-1.0343-6.47220.82832.998812.92180.0675-0.67120.2241-0.21030.1756-0.0193-0.60470.4734-0.24310.7459-0.3845-0.23380.70650.1730.453523.8639.944-64.179
54.2333-0.981-4.77660.67050.72669.57740.08310.1964-0.0596-0.1967-0.1678-0.22410.02560.04610.08460.2516-0.0559-0.04020.22020.06170.294521.3113.004-56.12
63.07011.4849-0.51513.9469-1.69734.06770.0417-0.0876-0.02840.0988-0.1816-0.08380.05990.34940.13980.3587-0.3997-0.21290.49170.25670.134626.35921.111-83.548
77.0597-1.73115.23143.0927-2.84888.1042-0.0678-0.7722-0.07230.09440.2381-0.08550.6769-0.4114-0.17040.7937-0.4412-0.08450.62990.25140.3996-18.205-35.823-14.622
85.12042.03525.17331.04951.255313.8209-0.21361.09-0.5536-0.35110.2697-0.12610.30311.5556-0.05610.5327-0.1179-0.2810.74830.11120.4917-13.364-11.889-8.109
92.69131.35570.34523.12041.35293.92510.0488-0.0685-0.0007-0.0077-0.11840.0793-0.1713-0.32560.06970.3286-0.3605-0.22090.46550.25030.1521-20.526-17.01-34.103
101.7721-2.0306-4.31436.85326.615911.70440.4202-0.23230.0463-0.8861-0.1544-0.2369-0.68650.4631-0.26580.8045-0.4233-0.20410.82910.2620.436512.348-0.848-11.924
110.1476-0.0167-0.75333.15353.5598.5321-0.0087-0.07050.0690.12890.11810.01980.07490.0511-0.10930.1902-0.0339-0.0740.38460.0060.2842-13.495-7.525-19.778
123.31521.5431.28533.33910.74563.2748-0.15560.07490.0377-0.12570.0540.0264-0.3035-0.09350.10160.4024-0.3753-0.21890.40460.22110.1362-6.619-0.8777.443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 93
2X-RAY DIFFRACTION2A161 - 193
3X-RAY DIFFRACTION3A94 - 160
4X-RAY DIFFRACTION3A195 - 294
5X-RAY DIFFRACTION4B8 - 93
6X-RAY DIFFRACTION5B161 - 193
7X-RAY DIFFRACTION6B94 - 160
8X-RAY DIFFRACTION6B195 - 294
9X-RAY DIFFRACTION7C8 - 93
10X-RAY DIFFRACTION8C161 - 193
11X-RAY DIFFRACTION9C94 - 160
12X-RAY DIFFRACTION9C195 - 294
13X-RAY DIFFRACTION10D8 - 93
14X-RAY DIFFRACTION11D161 - 193
15X-RAY DIFFRACTION12D94 - 160
16X-RAY DIFFRACTION12D195 - 294

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