3'-UMP (CHEBI:28895)

ChEBI > Main

CHEBI:28895 - 3'-UMP

Main

ChEBI Ontology

Automatic Xrefs

Reactions

Pathways

Models

ChEBI Name	3'-UMP

ChEBI ID	CHEBI:28895

Definition	A pyrimidine ribonucleoside 3'-monophosphate having uracil as the nucleobase.

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

Secondary ChEBI IDs	CHEBI:27229, CHEBI:46259, CHEBI:1361, CHEBI:556513

Supplier Information	ZINC000004095646

Download	Molfile XML SDF

more structures >>

Molfile

call loadScript javascripts\jsmol\core\package.js

call loadScript javascripts\jsmol\core\core.z.js -- required by ClazzNode

call loadScript javascripts\jsmol\J\awtjs2d\WebOutputChannel.js

Jmol JavaScript applet jmolApplet0_object__123970600297916__ initializing

getValue debug = null

getValue logLevel = null

getValue allowjavascript = null

AppletRegistry.checkIn(jmolApplet0_object__123970600297916__)

call loadScript javascripts\jsmol\core\corestate.z.js

viewerOptions:

{ "name":"jmolApplet0_object","applet":true,"documentBase":"https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:1361","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0_object__123970600297916__","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol.MyStatusListener object]","codeBase":"https://www.ebi.ac.uk/chebi/javascripts/jsmol/","syncId":"123970600297916","bgcolor":"#000" }

Jmol Version: 13.2.7 $Date: 2013-10-01 11:35:15 -0500 (Tue, 01 Oct 2013) $

java.vendor: j2s

java.version: 0.0

os.name: j2s

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0_object (signed)

starting HoverWatcher_1

getValue emulate = null

defaults = "Jmol"

getValue boxbgcolor = null

getValue bgcolor = #000

backgroundColor = "#000"

getValue ANIMFRAMECallback = null

getValue APPLETREADYCallback = Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

getValue ATOMMOVEDCallback = null

getValue CLICKCallback = null

getValue ECHOCallback = null

getValue ERRORCallback = null

getValue EVALCallback = null

getValue HOVERCallback = null

getValue LOADSTRUCTCallback = null

getValue MEASURECallback = null

getValue MESSAGECallback = null

getValue MINIMIZATIONCallback = null

getValue PICKCallback = null

getValue RESIZECallback = null

getValue SCRIPTCallback = null

getValue SYNCCallback = null

getValue STRUCTUREMODIFIEDCallback = null

getValue doTranslate = null

language=en_US

getValue popupMenu = null

getValue script = null

Jmol applet jmolApplet0_object__123970600297916__ ready

call loadScript javascripts\jsmol\core\corescript.z.js

call loadScript javascripts\jsmol\J\script\FileLoadThread.js

starting QueueThread0_2

script 1 started

starting HoverWatcher_3

starting HoverWatcher_4

The Resolver thinks Mol

U3P - Ideal conformer

Mrv1927 07272113523D

starting HoverWatcher_5

Time for openFile(U3P - Ideal conformer

Mrv1927 07272113523D

34 35 0 0 0 0 999 V2000

-0.1920 0.5010 -2.2380 N 0 0 0 0 0 0 0 0 0 0 0 0

0.1930 -0.7020 -2.6980 C 0 0 0 0 0 0 0 0 0 0 0 0

0.0020 -1.0440 -3.9860 N 0 0 0 0 0 0 0 0 0 0 0 0

-0.5720 -0.1750 -4.8420 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.9780 1.0970 -4.3710 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.7790 1.4110 -3.0740 C 0 0 0 0 0 0 0 0 0 0 0 0

0.7120 -1.4960 -1.9380 O 0 0 0 0 0 0 0 0 0 0 0 0

-0.7410 -0.4810 -6.0080 O 0 0 0 0 0 0 0 0 0 0 0 0

-0.7390 -0.1170 3.6540 P 0 0 1 0 0 5 0 0 0 0 0 0

-1.5080 0.7650 4.7590 O 0 0 0 0 0 0 0 0 0 0 0 0

0.5580 -0.5700 4.2000 O 0 0 0 0 0 0 0 0 0 0 0 0

-1.6360 -1.3980 3.2710 O 0 0 0 0 0 0 0 0 0 0 0 0

3.9060 0.3220 0.8460 O 0 0 0 0 0 0 0 0 0 0 0 0

2.6960 -0.2940 1.2890 C 0 0 1 0 0 0 0 0 0 0 0 0

1.5060 0.5980 0.9310 C 0 0 1 0 0 0 0 0 0 0 0 0

1.4250 0.7550 -0.4950 O 0 0 0 0 0 0 0 0 0 0 0 0

0.1950 -0.0620 1.3980 C 0 0 1 0 0 0 0 0 0 0 0 0

-0.4860 0.7720 2.3360 O 0 0 0 0 0 0 0 0 0 0 0 0

-0.6360 -0.2080 0.0970 C 0 0 1 0 0 0 0 0 0 0 0 0

-2.0090 0.1080 0.3320 O 0 0 0 0 0 0 0 0 0 0 0 0

0.0230 0.8420 -0.8300 C 0 0 2 0 0 0 0 0 0 0 0 0

0.2820 -1.9170 -4.3010 H 0 0 0 0 0 0 0 0 0 0 0 0

-1.4410 1.8060 -5.0420 H 0 0 0 0 0 0 0 0 0 0 0 0

-1.0830 2.3770 -2.6970 H 0 0 0 0 0 0 0 0 0 0 0 0

-1.6400 0.1960 5.5290 H 0 0 0 0 0 0 0 0 0 0 0 0

-2.4710 -1.0600 2.9200 H 0 0 0 0 0 0 0 0 0 0 0 0

4.6280 -0.2710 1.0910 H 0 0 0 0 0 0 0 0 0 0 0 0

2.5820 -1.2630 0.8020 H 0 0 0 0 0 0 0 0 0 0 0 0

2.7330 -0.4330 2.3700 H 0 0 0 0 0 0 0 0 0 0 0 0

1.6190 1.5730 1.4050 H 0 0 0 0 0 0 0 0 0 0 0 0

0.3960 -1.0400 1.8350 H 0 0 0 0 0 0 0 0 0 0 0 0

-0.5360 -1.2110 -0.3180 H 0 0 0 0 0 0 0 0 0 0 0 0

-2.4520 0.0900 -0.5260 H 0 0 0 0 0 0 0 0 0 0 0 0

-0.3600 1.8390 -0.6140 H 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

1 6 1 0 0 0 0

1 21 1 0 0 0 0

2 3 1 0 0 0 0

2 7 2 0 0 0 0

3 4 1 0 0 0 0

3 22 1 0 0 0 0

4 5 1 0 0 0 0

4 8 2 0 0 0 0

5 6 2 0 0 0 0

5 23 1 0 0 0 0

6 24 1 0 0 0 0

9 10 1 0 0 0 0

9 11 2 0 0 0 0

9 12 1 0 0 0 0

9 18 1 0 0 0 0

10 25 1 0 0 0 0

12 26 1 0 0 0 0

13 14 1 0 0 0 0

13 27 1 0 0 0 0

14 15 1 0 0 0 0

14 28 1 0 0 0 0

14 29 1 0 0 0 0

15 16 1 0 0 0 0

15 17 1 0 0 0 0

15 30 1 1 0 0 0

16 21 1 0 0 0 0

17 18 1 0 0 0 0

17 19 1 0 0 0 0

17 31 1 1 0 0 0

19 20 1 0 0 0 0

19 21 1 0 0 0 0

19 32 1 6 0 0 0

20 33 1 0 0 0 0

21 34 1 1 0 0 0

M END): 16 ms

reading 34 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

34 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Script completed

Jmol script terminated

Molfile expand

Formula

C9H13N2O9P

Net Charge

Average Mass

324.18136

Monoisotopic Mass

324.03587

InChI

InChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChIKey

FOGRQMPFHUHIGU-XVFCMESISA-N

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=CC(=O)NC1=O

Metabolite of Species	Details
Escherichia coli (NCBI:txid562)	See: PubMed

Roles Classification
Biological Role(s):	Escherichia coli metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.

View more via ChEBI Ontology

ChEBI Ontology
Outgoing	3'-UMP (CHEBI:28895) has role Escherichia coli metabolite (CHEBI:76971) 3'-UMP (CHEBI:28895) is a pyrimidine ribonucleoside 3'-monophosphate (CHEBI:37018) 3'-UMP (CHEBI:28895) is a uridine phosphate (CHEBI:27237) 3'-UMP (CHEBI:28895) is conjugate acid of 3'-UMP(2−) (CHEBI:60784)

Incoming	2'-deoxyuridine 3'-monophosphate (CHEBI:46322) has functional parent 3'-UMP (CHEBI:28895) 3'-UMP(2−) (CHEBI:60784) is conjugate base of 3'-UMP (CHEBI:28895)

IUPAC Name

3'-uridylic acid

Synonyms	Sources
3'-UMP	KEGG COMPOUND
3'-uridinemonophosphate	DrugBank
uridine 3'-(dihydrogen phosphate)	ChemIDplus
uridine 3'-monophosphate	KEGG COMPOUND
uridine 3'-phosphate	KEGG COMPOUND

Manual Xrefs	Databases
91753	ChemSpider
C01368	KEGG COMPOUND
DB02714	DrugBank
HMDB0060282	HMDB
U3P	PDBeChem
View more database links

Registry Number	Type	Source
84-53-7	CAS Registry Number	ChemIDplus

Citations

Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R, Wilamowski M, Kang S, Nicolaescu V, Randall G, Michalska K, Joachimiak A (2021)
Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.
Communications biology 4, 193 [PubMed:33564093]
[show Abstract]

Doamekpor SK, Gozdek A, Kwasnik A, Kufel J, Tong L (2020)
A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes.
Nucleic acids research 48, 349-358 [PubMed:31777937]
[show Abstract]

Gagné D, French RL, Narayanan C, Simonović M, Agarwal PK, Doucet N (2015)
Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity.
Structure (London, England : 1993) 23, 2256-2266 [PubMed:26655472]
[show Abstract]

Leonidas DD, Chavali GB, Oikonomakos NG, Chrysina ED, Kosmopoulou MN, Vlassi M, Frankling C, Acharya KR (2003)
High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.
Protein science : a publication of the Protein Society 12, 2559-2574 [PubMed:14573867]
[show Abstract]

Sica F, Di Fiore A, Zagari A, Mazzarella L (2003)
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative.
Proteins 52, 263-271 [PubMed:12833549]
[show Abstract]

Suzuki A, Yao M, Tanaka I, Numata T, Kikukawa S, Yamasaki N, Kimura M (2000)
Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity.
Biochemical and biophysical research communications 275, 572-576 [PubMed:10964705]
[show Abstract]

Fisher BM, Schultz LW, Raines RT (1998)
Coulombic effects of remote subsites on the active site of ribonuclease A.
Biochemistry 37, 17386-17401 [PubMed:9860854]
[show Abstract]
The active-site cleft of bovine pancreatic ribonuclease A (RNase A) is lined with cationic residues that interact with a bound nucleic acid. Those residues interacting with the phosphoryl groups comprise the P0, P1, and P2 subsites, with the scissile P-O5' bond residing in the P1 subsite. Coulombic interactions between the P0 and P2 subsites and phosphoryl groups of the substrate were characterized previously [Fisher, B. M., Ha, J.-H., and Raines, R. T. (1998) Biochemistry 37, 12121-12132]. Here, the interactions between these subsites and the active-site residues His12 and His119 are described in detail. A protein variant in which the cationic residues in these subsites (Lys66 in the P0 subsite and Lys7 and Arg10 in the P2 subsite) were replaced with alanine was crystallized, both free and with bound 3'-uridine monophosphate (3'-UMP). Structures of K7A/R10A/K66A RNase A and the K7A/R10A/K66A RNase A.3'-UMP complex were determined by X-ray diffraction analysis to resolutions of 2.0 and 2.1 A, respectively. There is little observable change between these structures and that of wild-type RNase A, either free or with bound 3'-cytidine monophosphate. K7A/R10A/K66A RNase A was evaluated for its ability to cleave UpA, a dinucleotide substrate that does not span the P0 or the P2 subsites. In comparison to the wild-type enzyme, the value of kcat was decreased by 5-fold and that of kcat/Km was decreased 10-fold, suggesting that these remote subsites interact with the active site. These interactions were characterized by determining the pKa values of His12 and His119 at 0.018 and 0.142 M Na+, both in wild-type RNase A and the K7A/R10A/K66A variant. The side chains of Lys7, Arg10, and Lys66 depress the pKa values of these histidine residues, and this depression is sensitive to the salt concentration. In addition, the P0 and P2 subsites influence the interaction of His12 and His119 with each other, as demonstrated by changes in the cooperativity that gives rise to microscopic pKa values. Finally, the affinity of 3'-UMP for wild-type RNase A and the K7A/R10A/K66A variant at 0.018 and 0.142 M Na+ was determined by isothermal titration calorimetry. 3'-UMP binds to the variant protein with 5-fold weaker affinity at 0.018 M Na+ and 3-fold weaker affinity at 0.142 M Na+ than it binds to wild-type RNase A. Together these data demonstrate that long-range Coulombic interactions are an important feature in catalysis by RNase A.

Last Modified

27 July 2021

CHEBI:28895 - 3'-UMP

ChEBI is part of the ELIXIR infrastructure