Chemical Components in the PDB

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CNU : Summary

Code

CNU

One-letter code

U

Molecule name

5-CYANO-URIDINE-5'-MONOPHOSPHATE

Synonyms

5-cyano-UMP
5-cyanouridine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 10.04 5-cyanouridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(5-cyano-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H12 N3 O9 P

Formal charge

0

Molecular weight

349.191 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 N#CC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C#N)C(=O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)C#N
Canonical SMILES CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C#N)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C#N

IUPAC InChI

InChI=1S/C10H12N3O9P/c11-1-4-2-13(10(17)12-8(4)16)9-7(15)6(14)5(22-9)3-21-23(18,19)20/h2,5-7,9,14-15H,3H2,(H,12,16,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1

IUPAC InChI key

BUHKUGLYORHFNN-JXOAFFINSA-N
CNU

wwPDB Information

Atom count

35 (23 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

U

Defined at

2007-12-14

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



CNU : Atoms of Molecule

Total Number of Atoms: 35
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1P O O1P N N N 0 -5.636 -0.193 -0.101
2 P P P N N N 0 -4.549 -1.144 0.224
3 O2P O O2P N N N 0 -4.983 -2.044 1.486
4 O3P O O3P N N Y 0 -4.272 -2.096 -1.044
5 O5' O O5' N N N 0 -3.21 -0.325 0.583
6 C5' C C5' N N N 0 -2.631 0.643 -0.294
7 C4' C C4' R N N 0 -1.374 1.229 0.352
8 O4' O O4' N N N 0 -0.325 0.237 0.4
9 C3' C C3' S N N 0 -0.801 2.367 -0.522
10 O3' O O3' N N N 0 -1.212 3.639 -0.02
11 C2' C C2' R N N 0 0.73 2.203 -0.394
12 O2' O O2' N N N 0 1.311 3.371 0.191
13 C1' C C1' R N N 0 0.901 0.986 0.542
14 N1 N N1 N N N 0 2.046 0.175 0.12
15 C2 C C2 N N N 0 2.037 -0.389 -1.098
16 O2 O O2 N N N 0 1.077 -0.212 -1.822
17 N3 N N3 N N N 0 3.057 -1.143 -1.544
18 C4 C C4 N N N 0 4.139 -1.359 -0.766
19 O4 O O4 N N N 0 5.065 -2.04 -1.165
20 C6 C C6 N N N 0 3.097 0.015 0.969
21 C5 C C5 N N N 0 4.174 -0.752 0.574
22 C52 C C52 N N N 0 5.296 -0.948 1.442
23 N53 N N53 N N N 0 6.186 -1.104 2.131
24 HO2P H HO2P N N N 0 -5.784 -2.566 1.341
25 HO3P H HO3P N N Y 0 -3.57 -2.745 -0.903
26 H5' H H5' N N N 0 -2.367 0.167 -1.238
27 H5'A H H5'A N N N 0 -3.35 1.442 -0.479
28 H4' H H4' N N N 0 -1.598 1.596 1.353
29 H3' H H3' N N N 0 -1.114 2.247 -1.559
30 HO3' H HO3' N N Y 0 -0.88 4.39 -0.531
31 H2' H H2' N N N 0 1.176 2.004 -1.369
32 HO2' H HO2' N N N 0 1.181 4.177 -0.326
33 H1' H H1' N N N 0 1.028 1.316 1.573
34 HN3 H HN3 N N N 0 3.015 -1.534 -2.43
35 H6 H H6 N N N 0 3.086 0.481 1.943



CNU : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1P P O P doub 1.48 N N
2 O2P P O P sing 1.61 N N
3 P O5' P O sing 1.61 N N
4 P O3P P O sing 1.61 N N
5 O2P HO2P O H sing 0.97 N N
6 O3P HO3P O H sing 0.97 N N
7 C5' O5' C O sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'A C H sing 1.09 N N
11 O4' C4' O C sing 1.44 N N
12 C4' C3' C C sing 1.55 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C2' C3' C C sing 1.55 N N
16 C3' O3' C O sing 1.43 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C1' C2' C C sing 1.54 N N
20 C2' O2' C O sing 1.43 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO2' O H sing 0.97 N N
23 N1 C1' N C sing 1.47 N N
24 C1' H1' C H sing 1.09 N N
25 C2 N1 C N sing 1.34 N N
26 N1 C6 N C sing 1.36 N N
27 N3 C2 N C sing 1.34 N N
28 O2 C2 O C doub 1.22 N N
29 N3 C4 N C sing 1.35 N N
30 N3 HN3 N H sing 0.97 N N
31 O4 C4 O C doub 1.22 N N
32 C4 C5 C C sing 1.47 N N
33 C5 C6 C C doub 1.38 N N
34 C6 H6 C H sing 1.08 N N
35 C5 C52 C C sing 1.43 N N
36 C52 N53 C N trip 1.14 N N



CNU : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
CNU 3bk0 Open in New Window Bound ligand 2 1
CNU 3ewz Open in New Window Bound ligand 4 1