Chemical Components in the PDB

pdbe.org/chem
spacer

RPC : Summary

Code

RPC

One-letter code

C

Molecule name

cytidine 3',5'-bis(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 cytidine 3',5'-bis(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] dihydrogen phosphate

Formula

C9 H15 N3 O11 P2

Formal charge

0

Molecular weight

403.176 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2OP(=O)(O)O
SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]2O
SMILES OpenEye OEToolkits 1.7.6 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)OP(=O)(O)O)O
Canonical SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)OP(=O)(O)O)O

IUPAC InChI

InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(14)11-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H2,10,11,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

MVGIITUCOOTSAP-XVFCMESISA-N
RPC

wwPDB Information

Atom count

40 (25 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

C

Defined at

2012-12-11

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



RPC : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 1.457 -0.632 -0.763
2 C2 C C2 N N N 0 3.082 0.596 0.566
3 C2' C C2' R N N 0 0.889 -1.495 0.392
4 C3' C C3' S N N 0 -0.637 -1.281 0.237
5 C4 C C4 N N N 0 5.349 0.572 0.118
6 C4' C C4' R N N 0 -0.754 0.028 -0.568
7 C5 C C5 N N N 0 5.121 -0.283 -0.98
8 C5' C C5' N N N 0 -1.559 1.058 0.228
9 C6 C C6 N N N 0 3.853 -0.668 -1.258
10 H1 H H1 N N N 0 -0.864 4.478 0.974
11 H10 H H10 N N N 0 5.944 -0.624 -1.589
12 H11 H H11 N N N 0 7.374 0.679 -0.117
13 H12 H H12 N N N 0 6.781 1.567 1.18
14 H14 H H14 N N N 0 -1.253 -4.649 1.243
15 H15 H H15 N N N 0 -3.682 -4.835 -0.764
16 H17 H H17 N N N 0 -3.156 5.402 -0.991
17 H2 H H2 N N N 0 -1.017 1.317 1.138
18 H3 H H3 N N N 0 -2.529 0.637 0.491
19 H4 H H4 N N N 0 -1.242 -0.165 -1.523
20 H5 H H5 N N N 0 -1.11 -1.172 1.213
21 H6 H H6 N N N 0 1.237 -1.131 1.358
22 H7 H H7 N N N 0 2.176 -3.056 0.303
23 H8 H H8 N N N 0 1.41 -1.175 -1.707
24 H9 H H9 N N N 0 3.653 -1.323 -2.094
25 N1 N N1 N N N 0 2.833 -0.222 -0.473
26 N3 N N3 N N N 0 4.325 0.98 0.855
27 N4 N N4 N N N 0 6.627 0.98 0.424
28 O2 O O2 N N N 0 2.157 0.99 1.255
29 O2' O O2' N N N 0 1.23 -2.872 0.215
30 O3' O O3' N N N 0 -1.224 -2.366 -0.484
31 O4' O O4' N N N 0 0.58 0.515 -0.789
32 O5' O O5' N N N 0 -1.748 2.231 -0.565
33 OP1 O OP1 N N N 0 -1.76 4.186 1.193
34 OP2 O OP2 N N N 0 -3.905 3.115 0.402
35 OP3 O OP3 N N Y 0 -2.681 4.596 -1.235
36 OP4 O OP4 N N N 0 -1.985 -4.036 1.398
37 OP5 O OP5 N N N 0 -3.575 -2.329 0.435
38 OP6 O OP6 N N N 0 -2.941 -4.278 -1.038
39 P P P N N N 0 -2.553 3.523 -0.042
40 P2 P P2 N N N 0 -2.456 -3.233 0.085



RPC : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP2 P O P doub 1.48 N N
2 OP5 P2 O P doub 1.48 N N
3 OP6 P2 O P sing 1.61 N N
4 OP1 P O P sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 C5' O5' C O sing 1.43 N N
7 C5' C4' C C sing 1.53 N N
8 P2 O3' P O sing 1.61 N N
9 P2 OP4 P O sing 1.61 N N
10 C3' C4' C C sing 1.54 N N
11 C3' O3' C O sing 1.43 N N
12 C3' C2' C C sing 1.55 N N
13 C4' O4' C O sing 1.44 N N
14 C2' O2' C O sing 1.43 N N
15 C2' C1' C C sing 1.55 N N
16 O4' C1' O C sing 1.44 N N
17 C1' N1 C N sing 1.46 N N
18 C6 N1 C N sing 1.36 N N
19 C6 C5 C C doub 1.35 N N
20 N1 C2 N C sing 1.35 N N
21 C5 C4 C C sing 1.41 N N
22 C2 O2 C O doub 1.22 N N
23 C2 N3 C N sing 1.33 N N
24 C4 N3 C N doub 1.33 N N
25 C4 N4 C N sing 1.38 N N
26 OP1 H1 O H sing 0.97 N N
27 C5' H2 C H sing 1.09 N N
28 C5' H3 C H sing 1.09 N N
29 C4' H4 C H sing 1.09 N N
30 C3' H5 C H sing 1.09 N N
31 C2' H6 C H sing 1.09 N N
32 O2' H7 O H sing 0.97 N N
33 C1' H8 C H sing 1.09 N N
34 C6 H9 C H sing 1.08 N N
35 C5 H10 C H sing 1.08 N N
36 N4 H11 N H sing 0.97 N N
37 N4 H12 N H sing 0.97 N N
38 OP4 H14 O H sing 0.97 N N
39 OP6 H15 O H sing 0.97 N N
40 P OP3 P O sing 1.61 N N
41 OP3 H17 O H sing 0.97 N N



RPC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RPC 4i67 Open in New Window Polymer component 1 1