Chemical Components in the PDB

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829 : Summary

Code

829

One-letter code

X

Molecule name

5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine

Systematic names

ProgramVersionName
ACDLabs 11.02 5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine
OpenEye OEToolkits 1.6.1 N-[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]pyridine-4-carboxamide

Formula

C15 H17 N5 O5

Formal charge

0

Molecular weight

347.326 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=C1N=C(N)C=CN1C2OC(C(O)C2O)CNC(=O)c3ccncc3
SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1)[CH]2O[CH](CNC(=O)c3ccncc3)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.7.0 c1cnccc1C(=O)NCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O
Canonical SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CNC(=O)c3ccncc3)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.7.0 c1cnccc1C(=O)NC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O

IUPAC InChI

InChI=1S/C15H17N5O5/c16-10-3-6-20(15(24)19-10)14-12(22)11(21)9(25-14)7-18-13(23)8-1-4-17-5-2-8/h1-6,9,11-12,14,21-22H,7H2,(H,18,23)(H2,16,19,24)/t9-,11-,12-,14-/m1/s1

IUPAC InChI key

XQXWUTWGJVGDNS-XIDUGBJDSA-N
829

wwPDB Information

Atom count

42 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-10-28

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



829 : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -2.936 0.418 0.465
2 C2 C C2 N N N 0 -3.044 0.806 -0.819
3 O2 O O2 N N N 0 -2.361 0.261 -1.67
4 N3 N N3 N N N 0 -3.884 1.776 -1.176
5 C4 C C4 N N N 0 -4.638 2.386 -0.271
6 N4 N N4 N N N 0 -5.503 3.386 -0.652
7 C5 C C5 N N N 0 -4.549 2.003 1.083
8 C6 C C6 N N N 0 -3.695 1.011 1.429
9 C07 C C07 N N N 0 3.391 -0.474 -0.739
10 C08 C C08 N Y N 0 4.244 1.014 1.088
11 C09 C C09 N Y N 0 5.245 1.817 1.599
12 C1' C C1* R N N 0 -2.004 -0.652 0.827
13 N10 N N10 N Y N 0 6.366 2.007 0.933
14 C11 C C11 N Y N 0 6.587 1.448 -0.24
15 C12 C C12 N Y N 0 5.639 0.631 -0.825
16 C13 C C13 N Y N 0 4.437 0.396 -0.152
17 O15 O O15 N N N 0 3.573 -0.995 -1.822
18 C2' C C2* R N N 0 -2.395 -1.969 0.121
19 O2' O O2* N N N 0 -3.138 -2.811 1.005
20 C3' C C3* S N N 0 -1.041 -2.621 -0.237
21 O3' O O3* N N N 0 -0.905 -3.884 0.416
22 C4' C C4* R N N 0 0.009 -1.621 0.296
23 O4' O O4* N N N 0 -0.678 -0.351 0.338
24 C5' C C5* N N N 0 1.206 -1.547 -0.655
25 N5' N N5* N N N 0 2.239 -0.687 -0.073
26 HN4 H HN4 N N N 0 -5.562 3.647 -1.584
27 HN4A H HN4A N N N 0 -6.053 3.83 0.012
28 H5 H H5 N N N 0 -5.156 2.49 1.832
29 H6 H H6 N N N 0 -3.609 0.699 2.46
30 H08 H H08 N N N 0 3.328 0.862 1.639
31 H09 H H09 N N N 0 5.107 2.295 2.557
32 H1' H H1* N N N 0 -1.987 -0.79 1.908
33 H11 H H11 N N N 0 7.52 1.632 -0.751
34 H12 H H12 N N N 0 5.826 0.176 -1.787
35 H2' H H2* N N N 0 -2.971 -1.762 -0.781
36 HO2' H HO2* N N N 0 -3.409 -3.651 0.613
37 H3' H H3* N N N 0 -0.945 -2.736 -1.316
38 HO3' H HO3* N N N 0 -1.577 -4.532 0.163
39 H4' H H4* N N N 0 0.335 -1.909 1.296
40 H5' H H5* N N N 0 1.61 -2.547 -0.808
41 H5'A H H5*A N N N 0 0.885 -1.134 -1.611
42 HN5' H HN5* N N N 0 2.094 -0.27 0.79



829 : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C6 N1 C N sing 1.36 N N
2 N1 C1' N C sing 1.46 N N
3 N1 C2 N C sing 1.35 N N
4 N3 C2 N C sing 1.33 N N
5 C2 O2 C O doub 1.22 N N
6 C4 N3 C N doub 1.33 N N
7 C5 C4 C C sing 1.41 N N
8 N4 C4 N C sing 1.38 N N
9 N4 HN4 N H sing 0.97 N N
10 N4 HN4A N H sing 0.97 N N
11 C5 C6 C C doub 1.35 N N
12 C5 H5 C H sing 1.08 N N
13 C6 H6 C H sing 1.08 N N
14 O15 C07 O C doub 1.22 N N
15 C13 C07 C C sing 1.48 N N
16 C07 N5' C N sing 1.35 N N
17 C09 C08 C C doub 1.38 N Y
18 C13 C08 C C sing 1.4 N Y
19 C08 H08 C H sing 1.08 N N
20 N10 C09 N C sing 1.32 N Y
21 C09 H09 C H sing 1.08 N N
22 C2' C1' C C sing 1.54 N N
23 C1' O4' C O sing 1.44 N N
24 C1' H1' C H sing 1.09 N N
25 C11 N10 C N doub 1.32 N Y
26 C11 C12 C C sing 1.38 N Y
27 C11 H11 C H sing 1.08 N N
28 C12 C13 C C doub 1.4 N Y
29 C12 H12 C H sing 1.08 N N
30 C3' C2' C C sing 1.54 N N
31 C2' O2' C O sing 1.43 N N
32 C2' H2' C H sing 1.09 N N
33 O2' HO2' O H sing 0.97 N N
34 O3' C3' O C sing 1.43 N N
35 C3' C4' C C sing 1.54 N N
36 C3' H3' C H sing 1.09 N N
37 O3' HO3' O H sing 0.97 N N
38 C5' C4' C C sing 1.53 N N
39 C4' O4' C O sing 1.44 N N
40 C4' H4' C H sing 1.09 N N
41 N5' C5' N C sing 1.46 N N
42 C5' H5' C H sing 1.09 N N
43 C5' H5'A C H sing 1.09 N N
44 N5' HN5' N H sing 0.97 N N



829 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
829 3ke1 Open in New Window Bound ligand 3 1