Chemical Components in the PDB

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16B : Summary

Code

16B

One-letter code

C

Molecule name

N-hydroxycytidine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 N-hydroxycytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 2.0.7 [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[4-(oxidanylamino)-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H14 N3 O9 P

Formal charge

0

Molecular weight

339.196 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC1OC(N2C=CC(=NC2=O)NO)C(O)C1O
SMILES CACTVS 3.385 ONC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 2.0.7 C1=CN(C(=O)N=C1NO)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.385 ONC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 2.0.7 C1=CN(C(=O)N=C1NO)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C9H14N3O9P/c13-6-4(3-20-22(17,18)19)21-8(7(6)14)12-2-1-5(11-16)10-9(12)15/h1-2,4,6-8,13-14,16H,3H2,(H,10,11,15)(H2,17,18,19)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

DYOUVDKCXLKHKY-XVFCMESISA-N
16B

wwPDB Information

Atom count

36 (22 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

C

Defined at

2012-10-18

Last modified at

2021-08-11

Status

Released

Obsoleted

Not Assigned



16B : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP1 O OAA N N N 0 3.702 -2.145 1.092
2 P P PAE N N N 0 4.165 -1.339 -0.06
3 OP3 O OAD N N Y 0 5.481 -0.512 0.359
4 OP2 O OAF N N N 0 4.515 -2.316 -1.291
5 O5' O O5' N N N 0 3.004 -0.315 -0.5
6 C5' C C5' N N N 0 2.401 0.613 0.405
7 C4' C C4' R N N 0 1.341 1.431 -0.336
8 O4' O O4' N N N 0 0.252 0.579 -0.728
9 C3' C C3' S N N 0 0.766 2.513 0.599
10 O3' O O3' N N N 0 0.998 3.815 0.059
11 C2' C C2' R N N 0 -0.751 2.207 0.645
12 O2' O O2' N N N 0 -1.517 3.413 0.598
13 C1' C C1' R N N 0 -0.953 1.37 -0.648
14 N1 N NAM N N N 0 -2.132 0.509 -0.526
15 C2 C CAL N N N 0 -2.146 -0.48 0.387
16 O2 O OAK N N N 0 -1.175 -0.647 1.106
17 N3 N NAG N N N 0 -3.204 -1.277 0.52
18 C6 C CAN N N N 0 -3.209 0.715 -1.334
19 C5 C CAI N N N 0 -4.293 -0.088 -1.211
20 C4 C CAH N N N 0 -4.274 -1.117 -0.248
21 N4 N NAB N N N 0 -5.361 -1.948 -0.102
22 OAC O OAC N N N 0 -5.338 -2.98 0.867
23 HOP3 H H1 N N Y 0 5.841 0.039 -0.349
24 HOP2 H H2 N N N 0 5.208 -2.962 -1.097
25 H5' H H3 N N N 0 1.932 0.068 1.224
26 H5'' H H4 N N N 0 3.164 1.281 0.802
27 H4' H H5 N N N 0 1.782 1.898 -1.216
28 H3' H H6 N N N 0 1.205 2.429 1.594
29 HO3' H H7 N N Y 0 0.657 4.535 0.608
30 H2' H H8 N N N 0 -1.003 1.623 1.53
31 HO2' H H9 N N N 0 -1.424 3.97 1.383
32 H1' H H10 N N N 0 -1.041 2.022 -1.517
33 H6 H H11 N N N 0 -3.199 1.511 -2.064
34 H5 H H12 N N N 0 -5.158 0.059 -1.841
35 H41 H H13 N N N 0 -6.143 -1.826 -0.663
36 H14 H H14 N N N 0 -6.146 -3.511 0.895



16B : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAC N4 O N sing 1.42 N N
2 N4 C4 N C sing 1.38 N N
3 C4 C5 C C sing 1.41 N N
4 C4 N3 C N doub 1.33 N N
5 C5 C6 C C doub 1.35 N N
6 N3 C2 N C sing 1.33 N N
7 C6 N1 C N sing 1.36 N N
8 C2 N1 C N sing 1.35 N N
9 C2 O2 C O doub 1.22 N N
10 N1 C1' N C sing 1.47 N N
11 O2' C2' O C sing 1.43 N N
12 C2' C1' C C sing 1.55 N N
13 C2' C3' C C sing 1.55 N N
14 C1' O4' C O sing 1.44 N N
15 O4' C4' O C sing 1.44 N N
16 OP1 P O P doub 1.48 N N
17 C3' C4' C C sing 1.54 N N
18 C3' O3' C O sing 1.43 N N
19 C5' C4' C C sing 1.53 N N
20 C5' O5' C O sing 1.43 N N
21 O5' P O P sing 1.61 N N
22 P OP3 P O sing 1.61 N N
23 P OP2 P O sing 1.61 N N
24 OP3 HOP3 O H sing 0.97 N N
25 OP2 HOP2 O H sing 0.97 N N
26 C5' H5' C H sing 1.09 N N
27 C5' H5'' C H sing 1.09 N N
28 C4' H4' C H sing 1.09 N N
29 C3' H3' C H sing 1.09 N N
30 O3' HO3' O H sing 0.97 N N
31 C2' H2' C H sing 1.09 N N
32 O2' HO2' O H sing 0.97 N N
33 C1' H1' C H sing 1.09 N N
34 C6 H6 C H sing 1.08 N N
35 C5 H5 C H sing 1.08 N N
36 N4 H41 N H sing 0.97 N N
37 OAC H14 O H sing 0.97 N N



16B : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
16B 4hib Open in New Window Bound ligand 2 1
16B 4hkp Open in New Window Bound ligand 1 1
16B 7ozv Open in New Window Polymer component 1 1