Structure of PDB 7kpm Chain A Binding Site BS01

Receptor Information
>7kpm Chain A (length=255) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIYVAIKTLKAGYSEK
QRRDFLSEASIMGQFDHPNIIRLEGVVTKSRPVMIITEFMENGALDSFLR
QNDGQFTVIQLVGMLRGIAAGMKYLAEMNYVHRDLAARNILVNSNLVCKV
SDFPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDV
INAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIR
NPASL
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain7kpm Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7kpm Identification of tetracycline combinations as EphB1 tyrosine kinase inhibitors for treatment of neuropathic pain.
Resolution1.608 Å
Binding residue
(original residue number in PDB)		I625 G626 A627 G628 E629 F630 V633 A649 K651 M700 L751
Binding residue
(residue number reindexed from 1)		I15 G16 A17 G18 E19 F20 V23 A39 K41 M90 L141
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D744 A746 R748 N749 D762 P787
Catalytic site (residue number reindexed from 1) D134 A136 R138 N139 D152 P154
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:7kpm, PDBe:7kpm, PDBj:7kpm
PDBsum7kpm
PubMed33627480
UniProtP54762|EPHB1_HUMAN Ephrin type-B receptor 1 (Gene Name=EPHB1)

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