Structure of PDB 8tr5 Chain A Binding Site BS01

Receptor Information

>8tr5 Chain A (length=553) Species: 10114 (Rattus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SWNDVFQYETNKVTRIQSVNYGTIKWILHMTVFSYVSFALMSDKLYQRKE
PLISSVHTKVKGVAEVTEKLVHGIFDTADYTLPLQGNSFFVMTNYLKSEG
QEQKLCPEYPSRGKQCHSDQGCIKGWMDPQSKGIQTGRCIPYDQKRKTCE
IFAWCPAEEGKEAPRPALLRSAENFTVLIKNNIDFPGHNYTTRNILPGMN
ISCTFHKTWNPQCPIFRLGDIFQEIGENFTEVAVQGGIMGIEIYWDCNLD
SWSHRCQPKYSFRRLDDKYTNESLFPGYNFRYAKYYKENGMEKRTLIKAF
GVRFDILVFGTGGKFDIIQLVVYIGSTLSYFGLATVCIDLIINTYASTCC
RSRVYPSCKCCEPCAVNEYYYRKKCEPIVEPKPTLKYVSFVDEPHIWMVD
QQLLGKSLQDVKGQEVPRPQTDFLELSRLDSPDWCQCGNCLPSQLPENRR
ALEELCCRRKPGQCITTSELFSKIVLSREALQLLLLYQEPLLALEGEAIN
SKLRHCAYRSYATWRFVSQDMADFAILPSCCRWKIRKEFPKTQGQYSGFK
YPY

Ligand information

Ligand ID

GDP

InChI

InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

QGWNDRXFNXRZMB-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N

Formula

C10 H15 N5 O11 P2

Name

GUANOSINE-5'-DIPHOSPHATE

PDB chain

8tr5 Chain A Residue 701 [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	8tr5 High-affinity agonism at the P2X7 receptor is mediated by three residues outside the orthosteric pocket
Resolution	2.53 Å
Binding residue (original residue number in PDB)	R546 H547 Y550 A567 L569 R574 K583 Y588 S589 G590
Binding residue (residue number reindexed from 1)	R504 H505 Y508 A525 L527 R532 K541 Y546 S547 G548
Annotation score	4

External links

PDB	RCSB:8tr5, PDBe:8tr5, PDBj:8tr5
PDBsum	8tr5
PubMed	39107314
UniProt	Q64663\|P2RX7_RAT P2X purinoceptor 7 (Gene Name=P2rx7)

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