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- PDB-9nbs: Structure of HPK1 with compound R2 -

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Basic information

Entry
Database: PDB / ID: 9nbs
TitleStructure of HPK1 with compound R2
ComponentsMitogen-activated protein kinase kinase kinase kinase 1
KeywordsSIGNALING PROTEIN / kinase / cancer / inhibitor / HDX / molecular dynamics
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 / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / cell population proliferation / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / positive regulation of MAPK cascade / 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 / CNH domain / Citron homology (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. ...Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (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
: / Mitogen-activated protein kinase kinase kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKiefer, J.R. / Walters, B.T. / Wang, W. / Wu, P. / Duo, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.
Authors: Walters, B.T. / Patapoff, A.W. / Kiefer, J.R. / Wu, P. / Wang, W.
History
DepositionFeb 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,53724
Polymers70,0372
Non-polymers2,50022
Water10,016556
1
A: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,41613
Polymers35,0181
Non-polymers1,39812
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)36,12011
Polymers35,0181
Non-polymers1,10210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.047, 58.075, 61.646
Angle α, β, γ (deg.)70.00, 66.51, 68.09
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35018.434 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 578 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1BW4 / (1R,3S,5'P)-4'-chloro-3-methyl-5'-[(3M)-3-(1-methyl-2-oxo-1,2-dihydropyridin-3-yl)phenyl]-1',2'-dihydrospiro[cyclopentane-1,3'-pyrrolo[2,3-b]pyridine]-3-carboxamide


Mass: 448.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: as described

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Data collection

DiffractionMean temperature: 91 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→52.47 Å / Num. obs: 54159 / % possible obs: 97.1 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.069 / Net I/σ(I): 9.8 / Num. measured all: 108089
Reflection shellResolution: 1.8→1.89 Å / % possible obs: 95.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.374 / Num. measured all: 15492 / Num. unique obs: 7760 / CC1/2: 0.697 / Rpim(I) all: 0.374 / Rrim(I) all: 0.528 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→52.47 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 2675 4.94 %
Rwork0.1651 --
obs0.1672 54144 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→52.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 165 556 5261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044862
X-RAY DIFFRACTIONf_angle_d0.9486573
X-RAY DIFFRACTIONf_dihedral_angle_d14.0861816
X-RAY DIFFRACTIONf_chiral_restr0.044722
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.28051100.24132666X-RAY DIFFRACTION96
1.83-1.860.30031040.22962749X-RAY DIFFRACTION96
1.86-1.90.25091440.23192622X-RAY DIFFRACTION96
1.9-1.940.28891560.22032687X-RAY DIFFRACTION96
1.94-1.990.28641540.20662693X-RAY DIFFRACTION96
1.99-2.040.26721540.19052637X-RAY DIFFRACTION96
2.04-2.090.22821450.18332703X-RAY DIFFRACTION97
2.09-2.150.21931530.17072727X-RAY DIFFRACTION97
2.15-2.220.23891240.16932716X-RAY DIFFRACTION97
2.22-2.30.22091460.16842677X-RAY DIFFRACTION97
2.3-2.40.18381620.15132690X-RAY DIFFRACTION97
2.4-2.510.20581690.15092685X-RAY DIFFRACTION97
2.51-2.640.20321370.15182779X-RAY DIFFRACTION98
2.64-2.80.19091250.15872723X-RAY DIFFRACTION98
2.8-3.020.1981290.16332728X-RAY DIFFRACTION98
3.02-3.320.19681080.16172760X-RAY DIFFRACTION98
3.32-3.80.20811180.14352775X-RAY DIFFRACTION98
3.8-4.790.15451580.13462743X-RAY DIFFRACTION99
4.79-52.470.1991790.1742709X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / 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)
10.0270.00880.01140.0110.02730.0105-0.11460.08190.11650.1203-0.13370.17390.1762-0.11410-0.0080.0574-0.0718-00.1291-0.0173-12.939546.198515.3479
2-0.0042-0.00250.0018-0.00260.0063-0.0018-0.021-0.0274-0.009-0.0122-0.0291-0.00580.01160.0387-00.0497-0.01870.05150.0494-0.2338-0.1045-20.489927.7665-4.321
30.02260.00390.0020.0151-0.00490.0155-0.05130.13230.03360.0606-0.01840.00010.0279-0.081200.07470.00510.00710.0022-0.050.0699-32.709135.40122.1513
4-0.0017-0.0280.01210.00770.00960.02160.0121-0.15-0.0842-0.1967-0.15080.0070.08080.0019-00.0405-0.01420.04520.06950.13510.0128-10.30921.9272-11.6685
50.0038-0.00550.00280.0022-0.00550.00560.0279-0.1304-0.0195-0.0658-0.0026-0.00830.04320.035500.067-0.01090.00910.1269-0.00190.0694-18.450610.2013-7.6713
60.00160.0003-0.0019-0.00040.0020.0010.00120.021-0.00320.00710.0211-0.00560.00680.009600.07540.0027-0.00790.1018-0.16450.0508-24.349924.219710.5674
70.04430.01880.00250.01210.0051-0.00310.0312-0.1079-0.0528-0.04670.0763-0.009-0.0624-0.109700.0555-0.0428-0.0027-0.0594-0.1209-0.054-31.406313.9062-19.4856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 156 )
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 193 )
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 293 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 130 )
5X-RAY DIFFRACTION5chain 'B' and (resid 131 through 171 )
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 193 )
7X-RAY DIFFRACTION7chain 'B' and (resid 194 through 293 )

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