Chemical Components in the PDB

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IC : Summary

Code

IC

One-letter code

C

Molecule name

ISOCYTIDINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 2-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidin-4(1H)-one
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2-amino-4-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H14 N3 O8 P

Formal charge

0

Molecular weight

323.197 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O)N
SMILES CACTVS 3.341 NC1=NC(=O)C=CN1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=NC1=O)N)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 NC1=NC(=O)C=CN1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=NC1=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C9H14N3O8P/c10-9-11-5(13)1-2-12(9)8-7(15)6(14)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,14-15H,3H2,(H2,10,11,13)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

ONSQLDCEJIIUJS-XVFCMESISA-N
IC

wwPDB Information

Atom count

35 (21 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

C

Defined at

2000-11-07

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



IC : 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 P P P N N N 0 0.932 -0.079 -4.192
2 OP1 O O1P N N N 0 1.62 1.199 -3.904
3 OP2 O O2P N N N 0 1.974 -1.112 -4.855
4 OP3 O O3P N N Y 0 -0.284 0.183 -5.212
5 O5' O O5* N N N 0 0.359 -0.7 -2.821
6 O3' O O3* N N N 0 -3.437 0.488 -0.64
7 C1' C C1* R N N 0 -0.755 -0.488 1.279
8 C2' C C2* R N N 0 -1.815 0.63 1.185
9 C3' C C3* S N N 0 -2.071 0.776 -0.332
10 C4' C C4* R N N 0 -1.138 -0.274 -0.974
11 C5' C C5* N N N 0 -0.554 0.256 -2.284
12 O4' O O4* N N N 0 -0.089 -0.478 -0.002
13 O2' O O2* N N N 0 -3.015 0.25 1.861
14 N2 N N2 N N N 0 -1.169 -1.386 3.857
15 C4 C C4 N N N 0 1.916 0.303 4.38
16 N3 N N3 N N N 0 0.802 -0.409 4.594
17 C2 C C2 N N N 0 -0.038 -0.654 3.609
18 O4 O O4 N N N 0 2.69 0.525 5.299
19 N1 N N1 N N N 0 0.199 -0.198 2.352
20 C6 C C6 N N N 0 1.317 0.537 2.084
21 C5 C C5 N N N 0 2.191 0.799 3.08
22 HOP2 H 2HOP N N N 0 2.293 -0.702 -5.671
23 HOP3 H 3HOP N N N 0 -0.704 -0.673 -5.373
24 HO3' H H3T N N Y 0 -3.97 1.173 -0.216
25 H1' H H1* N N N 0 -1.234 -1.452 1.45
26 H2' H H2* N N N 0 -1.424 1.561 1.597
27 H3' H H3* N N N 0 -1.808 1.778 -0.671
28 H4' H H4* N N N 0 -1.678 -1.204 -1.149
29 H5' H 1H5* N N N 0 -1.36 0.429 -2.997
30 H5'' H 2H5* N N N 0 -0.03 1.193 -2.095
31 HO2' H 2HO* N N N 0 -3.655 0.96 1.715
32 H21 H 1H2 N N N 0 -1.264 -1.863 4.696
33 H22 H 2H2 N N N 0 -1.877 -1.424 3.194
34 H6 H H6 N N N 0 1.503 0.903 1.085
35 H5 H H5 N N N 0 3.084 1.375 2.889



IC : 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 P OP1 P O doub 1.48 N N
2 P OP2 P O sing 1.61 N N
3 P OP3 P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 OP2 HOP2 O H sing 0.97 N N
6 OP3 HOP3 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 O3' C3' O C sing 1.43 N N
9 O3' HO3' O H sing 0.97 N N
10 C1' C2' C C sing 1.54 N N
11 C1' O4' C O sing 1.44 N N
12 C1' N1 C N sing 1.46 N N
13 C1' H1' C H sing 1.09 N N
14 C2' C3' C C sing 1.55 N N
15 C2' O2' C O sing 1.43 N N
16 C2' H2' C H sing 1.09 N N
17 C3' C4' C C sing 1.54 N N
18 C3' H3' C H sing 1.09 N N
19 C4' C5' C C sing 1.53 N N
20 C4' O4' C O sing 1.44 N N
21 C4' H4' C H sing 1.09 N N
22 C5' H5' C H sing 1.09 N N
23 C5' H5'' C H sing 1.09 N N
24 O2' HO2' O H sing 0.97 N N
25 N2 C2 N C sing 1.37 N N
26 N2 H21 N H sing 0.97 N N
27 N2 H22 N H sing 0.97 N N
28 C4 N3 C N sing 1.34 N N
29 C4 O4 C O doub 1.22 N N
30 C4 C5 C C sing 1.42 N N
31 N3 C2 N C doub 1.32 N N
32 C2 N1 C N sing 1.36 N N
33 N1 C6 N C sing 1.36 N N
34 C6 C5 C C doub 1.35 N N
35 C6 H6 C H sing 1.08 N N
36 C5 H5 C H sing 1.08 N N



IC : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
IC 1g3a Open in New Window Polymer component 2 1
IC 2o81 Open in New Window Polymer component 2 1
IC 2o83 Open in New Window Polymer component 2 1