Structure of PDB 5dzc Chain A Binding Site BS01

Receptor Information
>5dzc Chain A (length=816) Species: 126793 (Plasmodium vivax Sal-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GMRCNEKKKAIFSNSGEDTLMEDHLQLREKLSEDIEMIKASLKNNLVCST
LNDNEILTLSNYMQFFVFKGGDLVIKQGEKGSYFFIINSGKFDVYVNDKK
VKSMGKGSSFGEAALIHNTQRSATIMAETDGTLWGVQRSTFRATLKQLSN
RNFNENRSFIDSVSVFDMLTEAQKNMITNACVIQMFKPGETIVKQGDYGD
VLFILKEGKATVFINDKEIRVLNKGSYFGERALLYDEPRSATIIAKEPTA
CASICRKLLNIVLGNLQVVLFRNIMTEALQQSEIFRQFSAEQLNDLADTA
IVRDYPANYHILHKKSVKYLIVLEGKVELFLDDESIGILTRGKSFGDQYV
LNQKQKFRHTVKSLDVCKIALITESCLADCLGDNNIDASIDHNNKKSIIK
KMYIFRYLSEQQCNLLIEAFRTTRYEEGDYIIQEGEVGSRFYIIKNGEVE
VTKNGKRLRTLGKNDYFGERALLYDEPRTASIISKATSVECWFVDKSVFL
QIIQGPMLTHLEERIKMQDTKVEMHELETERIIGRGTFGTVKLVHHKPTQ
IRYALKCVSKRSIISLNQQNNIKLEREITAENDHPFIIRLVRTFKDSNCF
YFLTELVTGGELYDAIRKLGLLSKPQAQFYLGSIILAIEYLHERNIVYRD
LKPENILLDKQGYVKLIDFGCAKKIQGRAYTLVGTPHYMAPEVILGKGYG
CTVDIWALGVCLYEFICGPLPFGNDQEDQLEIFRDILTGQLTFPDYVSDQ
DSINLMKRLLCRLPQGRIGCSINGFKDIKEHAFFGNFNWDKLAGRLLEPP
LVSKGETYAEDIDSWD
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5dzc Chain A Residue 1001 [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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PDB5dzc Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I540 G543 V548 A561 K563 V614 E618 L664 D675
Binding residue
(residue number reindexed from 1)		I533 G536 V541 A554 K556 V607 E611 L657 D668
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D657 K659 N662 D675 T692
Catalytic site (residue number reindexed from 1) D650 K652 N655 D668 T685
Enzyme Commision number 2.7.11.12: cGMP-dependent protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004691 cAMP-dependent protein kinase activity
GO:0004692 cGMP-dependent protein kinase activity
GO:0005524 ATP binding
GO:0030553 cGMP binding
GO:0046872 metal ion binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007165 signal transduction
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005952 cAMP-dependent protein kinase complex
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dzc, PDBe:5dzc, PDBj:5dzc
PDBsum5dzc
PubMed31239348
UniProtA5K0N4|KGP_PLAVS cGMP-dependent protein kinase (Gene Name=PKG)

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