Structure of PDB 5tha Chain A Binding Site BS01

Receptor Information

>5tha Chain A (length=684) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTP
PFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVV
TEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPR
TIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIA
WCPLPGEGCYLATGSKDQTIRIWSCSRGRGVMILKLPFLKRRGGGIDPTV
KERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQSRRKYTLFSASSEGQN
HSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFA
YSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTAL
CWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPV
PPMSLSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVH
TEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHE
HGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHT
AKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHQGRLLCVA
WSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQG

Ligand information

Ligand ID

GP3

InChI

InChI=1S/C20H27N10O18P3/c21-19-25-13-7(15(35)27-19)23-3-29(13)17-11(33)9(31)5(45-17)1-43-49(37,38)47-51(41,42)48-50(39,40)44-2-6-10(32)12(34)18(46-6)30-4-24-8-14(30)26-20(22)28-16(8)36/h3-6,9-12,17-18,31-34H,1-2H2,(H,37,38)(H,39,40)(H,41,42)(H3,21,25,27,35)(H3,22,26,28,36)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1

InChIKey

AAXYAFFKOSNMEB-MHARETSRSA-N

SMILES

Software	SMILES
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)[CH](O)[CH]3O

Formula

C20 H27 N10 O18 P3

Name

DIGUANOSINE-5'-TRIPHOSPHATE

PDB chain

5tha Chain A Residue 822 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5tha Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly.
Resolution	1.8 Å
Binding residue (original residue number in PDB)	Y474 T540 N582 Y660
Binding residue (residue number reindexed from 1)	Y442 T501 N543 Y621
Annotation score	1
Binding affinity	MOAD: Kd=140uM PDBbind-CN: -logKd/Ki=3.85,Kd=140uM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5tha, PDBe:5tha, PDBj:5tha
PDBsum	5tha
PubMed	27881600
UniProt	Q8TEQ6\|GEMI5_HUMAN Gem-associated protein 5 (Gene Name=GEMIN5)

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