Structure of PDB 5od2 Chain A Binding Site BS02

Receptor Information
>5od2 Chain A (length=456) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIKKFIETIKGTKLFTAYNTNVDAIKYLKDEDVQKLVDEFNHKDIIERME
EYPRIIEEPLDFVARLVHSIKTGKPAEVPIKDDKKLHEWFDRIKYDEERM
GGQAGIVSNLMATLQIDKIIVYTPFLSKKQAEMFVDYDNLLYPLVENGNL
VLKKVREAYRDDPIKINRIFEFKKGLKFKLNGEEITAKQSTRFIVASRPE
ALRIEIKDDVRKFLPKIGEAVDCAFLSGYQAIKEEYRDGKTAKYYFERAE
EDIKLLKKNKNIKTHLEFASISNIEIRKMVVDYILSNVESVGMDETEIAN
VLHILGYDELSNNILKDSFIEDVIEGAKILLDKFKNLEVVQVHTIYYILF
VCRADNPLSKEELEECLEFSTILASTKAKLGNIRAIDDLHEGLKIPHNKY
GDLLKEIAEKFNDNNYKIALSPSRYVEKPKSTVGLGDTISSGAFVYYVSL
LNKKRM
Ligand information
Ligand ID5ID
InChIInChI=1S/C11H13IN4O4/c12-4-1-16(10-6(4)9(13)14-3-15-10)11-8(19)7(18)5(2-17)20-11/h1,3,5,7-8,11,17-19H,2H2,(H2,13,14,15)/t5-,7-,8-,11-/m1/s1
InChIKeyWHSIXKUPQCKWBY-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)I
CACTVS 3.341Nc1ncnc2n(cc(I)c12)[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 10.04Ic2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
CACTVS 3.341Nc1ncnc2n(cc(I)c12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)I
FormulaC11 H13 I N4 O4
Name(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL;
5-IODOTUBERCIDIN
ChEMBLCHEMBL99203
DrugBankDB04604
ZINCZINC000005161616
PDB chain5od2 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5od2 Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii in complex with 5-iodotubercidin reveals phosphoryl transfer mechanism.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		T349 A383 S428 Y430 V431 P434 L440 I444
Binding residue
(residue number reindexed from 1)		T344 A378 S423 Y425 V426 P429 L435 I439
Annotation score2
Binding affinityMOAD: Ki=0.74mM
Enzymatic activity
Enzyme Commision number 2.7.1.146: ADP-specific phosphofructokinase.
2.7.1.147: ADP-specific glucose/glucosamine kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008443 phosphofructokinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0043843 ADP-specific glucokinase activity
GO:0043844 ADP-specific phosphofructokinase activity
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006000 fructose metabolic process
GO:0006096 glycolytic process
GO:0016310 phosphorylation
GO:0046835 carbohydrate phosphorylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5od2, PDBe:5od2, PDBj:5od2
PDBsum5od2
PubMed29352744
UniProtQ58999|K6PF_METJA Bifunctional ADP-specific glucokinase/phosphofructokinase (Gene Name=pfkC)

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