3'-phosphate-adenosine-5'-diphosphate (CHEBI:44672)

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CHEBI:44672 - 3'-phosphate-adenosine-5'-diphosphate

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ChEBI Name	3'-phosphate-adenosine-5'-diphosphate

ChEBI ID	CHEBI:44672

Definition	An adenosine 3'-phosphate that is ADP carrying a phospate group at the 3'-position. It is potent inhibitor of bovine pancreatic ribonuclease A.

Stars	This entity has been manually annotated by the ChEBI Team.

Supplier Information	We are unable to retrieve the vendor information for this entry at this time. Please try again later.

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47 49 0 0 0 0 999 V2000

-1.9920 0.0930 -5.6760 P 0 0 2 0 0 0 0 0 0 0 0 0

-2.2660 -1.3480 -5.4840 O 0 0 0 0 0 0 0 0 0 0 0 0

-3.1810 0.7550 -6.5360 O 0 0 0 0 0 0 0 0 0 0 0 0

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-2.5500 -1.3070 3.8730 N 0 0 0 0 0 0 0 0 0 0 0 0

-2.2160 -0.5010 4.9100 C 0 0 0 0 0 0 0 0 0 0 0 0

-2.6520 -0.3700 6.2400 C 0 0 0 0 0 0 0 0 0 0 0 0

-3.6370 -1.2000 6.7470 N 0 0 0 0 0 0 0 0 0 0 0 0

-2.0920 0.5640 7.0010 N 0 0 0 0 0 0 0 0 0 0 0 0

-1.1520 1.3600 6.5250 C 0 0 0 0 0 0 0 0 0 0 0 0

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4.6090 -1.3820 1.7790 H 0 0 0 0 0 0 0 0 0 0 0 0

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-0.7240 2.1070 7.1780 H 0 0 0 0 0 0 0 0 0 0 0 0

-0.5490 0.7870 -1.9860 O 0 0 0 0 0 0 0 0 0 0 0 0

0.5270 0.1190 -1.3260 C 0 0 0 0 0 0 0 0 0 0 0 0

0.7220 0.7190 0.0670 C 0 0 1 0 0 0 0 0 0 0 0 0

-0.4660 0.5360 0.8650 O 0 0 0 0 0 0 0 0 0 0 0 0

1.8310 -0.0370 0.8300 C 0 0 1 0 0 0 0 0 0 0 0 0

3.0700 0.6680 0.7450 O 0 0 0 0 0 0 0 0 0 0 0 0

1.3250 -0.0710 2.2920 C 0 0 1 0 0 0 0 0 0 0 0 0

2.2380 0.6100 3.1540 O 0 0 0 0 0 0 0 0 0 0 0 0

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9 12 1 0 0 0 0

11 23 1 0 0 0 0

12 24 1 0 0 0 0

13 14 4 0 0 0 0

13 22 4 0 0 0 0

14 15 4 0 0 0 0

14 25 1 0 0 0 0

15 16 4 0 0 0 0

16 17 4 0 0 0 0

16 22 4 0 0 0 0

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32 9 1 0 0 0 0

33 34 1 0 0 0 0

33 35 1 0 0 0 0

33 43 1 0 0 0 0

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35 13 1 0 0 0 0

35 45 1 0 0 0 0

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reading 47 atoms

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47 atoms created

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Formula

C10H16N5O13P3

Net Charge

Average Mass

507.181

Monoisotopic Mass

506.99575

InChI

InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-31(23,24)28-30(20,21)22/h2-4,6-7,10,16H,1H2,(H,23,24)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1

InChIKey

GBBWIZKLHXYJOA-KQYNXXCUSA-N

SMILES

NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](OP(O)(O)=O)[C@H]1O

ChEBI Ontology
Outgoing	3'-phosphate-adenosine-5'-diphosphate (CHEBI:44672) has functional parent ADP (CHEBI:16761) 3'-phosphate-adenosine-5'-diphosphate (CHEBI:44672) is a adenosine 3'-phosphate (CHEBI:37097) 3'-phosphate-adenosine-5'-diphosphate (CHEBI:44672) is a adenosine 5'-phosphate (CHEBI:37096)

Incoming	coenzyme A (CHEBI:15346) has functional parent 3'-phosphate-adenosine-5'-diphosphate (CHEBI:44672)

IUPAC Name

adenosine 3'-(dihydrogen phosphate) 5'-(trihydrogen diphosphate)

Synonyms	Sources
5'-diphosphoadenosine 3'-phosphate	ChEBI
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methyl phosphono hydrogen phosphate	PDBeChem
adenosine 3'-phosphate 5'-diphosphate	ChEBI

Manual Xref	Database
PAP	PDBeChem
View more database links

Registry Number	Type	Source
13400-10-7	CAS Registry Number	ChEBI

Citations

Leonidas DD, Shapiro R, Irons LI, Russo N, Acharya KR (1999)
Toward rational design of ribonuclease inhibitors: high-resolution crystal structure of a ribonuclease A complex with a potent 3',5'-pyrophosphate-linked dinucleotide inhibitor.
Biochemistry 38, 10287-10297 [PubMed:10441122]
[show Abstract]
The crystal structure of ribonuclease A (RNase A) in complex with pdUppA-3'-p [5'-phospho-2'-deoxyuridine-3'-pyrophosphate (P'-->5') adenosine 3'-phosphate] has been determined at 1.7 A resolution. This dinucleotide is the most potent low molecular weight inhibitor of RNase A reported to date (K(i) = 27 nM) and is also effective against two major nonpancreatic RNases: eosinophil-derived neurotoxin and RNase-4; in all cases, tight binding in large part derives from the unusual 3',5'-pyrophosphate internucleotide linkage [Russo, N., and Shapiro, R. (1999) J. Biol. Chem. 274, 14902-14908]. The design of pdUppA-3'-p was based on the crystal structure of RNase A complexed with 5'-diphosphoadenosine 3'-phosphate (ppA-3'-p) [Leonidas, D. D., Shapiro, R., Irons, L. I., Russo, N., and Acharya, K. R. (1997) Biochemistry 36, 5578-5588]. The adenosine of pdUppA-3'-p adopts an atypical syn conformation not observed for standard adenosine nucleotides bound to RNase A. This conformation, which allows extensive interactions with Asn 67, Gln 69, Asn 71, and His 119, is associated with the placement of the 5'-beta-phosphate of the adenylate, rather than alpha-phosphate, at the site where substrate phosphodiester bond cleavage occurs. The contacts of the deoxyuridine 5'-phosphate portion of pdUppA-3'-p appear to be responsible for the 9-fold increased affinity of this compound as compared to ppA-3'-p: the uracil base binds to Thr 45 in the same manner as previous pyrimidine inhibitors, and the terminal 5'-phosphate is positioned to form medium-range Coulombic interactions with Lys 66. The full potential benefit of these added interactions is not realized because of compensatory losses of hydrogen bonds of Lys 7 and Gln 11 with the terminal 3'-phosphate and the adenylate 5'-alpha-phosphate, which were not predicted by modeling. The results reported here have important implications for the design of improved inhibitors of RNase A and for the development of therapeutic agents to control the activities of RNase homologues such as eosinophil-derived neurotoxin and angiogenin that have roles in human pathologies.

Russo N, Shapiro R (1999)
Potent inhibition of mammalian ribonucleases by 3', 5'-pyrophosphate-linked nucleotides.
The Journal of biological chemistry 274, 14902-14908 [PubMed:10329690]
[show Abstract]

Russo N, Shapiro R, Vallee BL (1997)
5'-Diphosphoadenosine 3'-phosphate is a potent inhibitor of bovine pancreatic ribonuclease A.
Biochemical and biophysical research communications 231, 671-674 [PubMed:9070868]
[show Abstract]

Leonidas DD, Shapiro R, Irons LI, Russo N, Acharya KR (1997)
Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution.
Biochemistry 36, 5578-5588 [PubMed:9154942]
[show Abstract]
High-resolution (1.7 A) crystal structures have been determined for bovine pancreatic ribonuclease A (RNase A) complexed with 5'-diphosphoadenosine 3'-phosphate (ppA-3'-p) and 5'-diphosphoadenosine 2'-phosphate (ppA-2'-p), as well as for a native structure refined to 2.0 A. These nucleotide phosphates are the two most potent inhibitors of RNase A reported so far, with Ki values of 240 and 520 nM, respectively. The binding modes and conformations of ppA-3'-p and ppA-2'-p were found to differ markedly from those anticipated on the basis of earlier structures of RNase A complexes. The key difference is that the 5'-beta-phosphate rather than the 5'-alpha-phosphate of each inhibitor occupies the P1 phosphate binding site. As a consequence, the ribose moieties of the two nucleotides are shifted by approximately 2 A compared to the positions of their counterparts in earlier complexes, and the adenine rings are rotated into unusual syn conformations. Thus, the six-membered and five-membered rings of both adenines are reversed with respect to the others but nonetheless engage in extensive interactions with the residues that form the B2 purine binding site of RNase A. Despite the close structural similarity of the two inhibitors, the puckers of their furanose rings are different: C2'-endo and C3'-endo, respectively. Moreover, their 5'-alpha-phosphates and 3'(2')-monophosphates interact with largely different sets of RNase residues. The results of this crystallographic study emphasize the difficulties inherent in qualitative modeling of protein-inhibitor interactions and the compelling reasons for high-resolution structural studies in which quantitative design of improved inhibitors was enabled. The structures presented here provide a promising starting point for the rational design of tight-binding RNase inhibitors, which may be used as therapeutic agents in restraining the ribonucleolytic activities of RNase homologues such as angiogenin, eosinophil-derived neurotoxin, and eosinophil cationic protein.

Fierke CA, Jencks WP (1986)
Two functional domains of coenzyme A activate catalysis by coenzyme A transferase. Pantetheine and adenosine 3'-phosphate 5'-diphosphate.
The Journal of biological chemistry 261, 7603-7606 [PubMed:3458707]
[show Abstract]

Last Modified

03 June 2024

CHEBI:44672 - 3'-phosphate-adenosine-5'-diphosphate

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