Chemical Components in the PDB

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16B : Summary

Code

16B

One-letter code

X

Molecule name

N-hydroxycytidine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 N-hydroxycytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3S,4R,5R)-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)OCC2OC(N1C(=O)N=C(NO)C=C1)C(O)C2O
SMILES CACTVS 3.370 ONC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.7.6 C1=CN(C(=O)N=C1NO)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.370 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 1.7.6 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

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-10-18

Last modified at

2012-11-09

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



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 NAB O N sing 1.42 N N
2 NAB CAH N C sing 1.38 N N
3 CAH CAI C C sing 1.41 N N
4 CAH NAG C N doub 1.33 N N
5 CAI CAN C C doub 1.35 N N
6 NAG CAL N C sing 1.33 N N
7 CAN NAM C N sing 1.36 N N
8 CAL NAM C N sing 1.35 N N
9 CAL OAK C O doub 1.22 N N
10 NAM 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 OAA PAE 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' PAE O P sing 1.61 N N
22 PAE OAD P O sing 1.61 N N
23 PAE OAF P O sing 1.61 N N
24 OAD H1 O H sing 0.97 N N
25 OAF H2 O H sing 0.97 N N
26 C5' H3 C H sing 1.09 N N
27 C5' H4 C H sing 1.09 N N
28 C4' H5 C H sing 1.09 N N
29 C3' H6 C H sing 1.09 N N
30 O3' H7 O H sing 0.97 N N
31 C2' H8 C H sing 1.09 N N
32 O2' H9 O H sing 0.97 N N
33 C1' H10 C H sing 1.09 N N
34 CAN H11 C H sing 1.08 N N
35 CAI H12 C H sing 1.08 N N
36 NAB H13 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: 2
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