Chemical Components in the PDB

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CKB : Summary

Code

CKB

One-letter code

X

Molecule name

1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione

Synonyms

1-D-glucopyranosyl-thymine

Systematic names

ProgramVersionName
ACDLabs 10.04 1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 1.5.0 5-methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidine-2,4-dione

Formula

C11 H16 N2 O7

Formal charge

0

Molecular weight

288.254 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C(O)C2O)CO
SMILES CACTVS 3.341 CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 CC1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)O)O
Canonical SMILES CACTVS 3.341 CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O

IUPAC InChI

InChI=1S/C11H16N2O7/c1-4-2-13(11(19)12-9(4)18)10-8(17)7(16)6(15)5(3-14)20-10/h2,5-8,10,14-17H,3H2,1H3,(H,12,18,19)/t5-,6-,7+,8-,10-/m1/s1

IUPAC InChI key

RMXUFBPORJBBEZ-HPFNVAMJSA-N
CKB

wwPDB Information

Atom count

36 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-11-16

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CKB : 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 -0.267 0.136 0.575
2 C2 C C2 N N N 0 1.498 -0.191 -1.064
3 C2' C C2' R N N 0 -0.837 1.406 -0.063
4 C3' C C3' S N N 0 -2.33 1.505 0.262
5 C4 C C4 N N N 0 3.76 -0.247 -0.484
6 C4' C C4' S N N 0 -3.035 0.239 -0.234
7 C5 C C5 N N N 0 3.406 -0.043 0.872
8 C5' C C5' R N N 0 -2.381 -0.986 0.41
9 C6 C C6 N N N 0 2.102 0.08 1.199
10 C6' C C6' N N N 0 -3.04 -2.258 -0.126
11 C7 C C7 N N N 0 4.47 0.037 1.936
12 H1' H H1' N N N 0 -0.366 0.197 1.658
13 H2' H H2' N N N 0 -0.701 1.363 -1.144
14 H3' H H3' N N N 0 -2.464 1.598 1.34
15 H4' H H4' N N N 0 -2.944 0.172 -1.319
16 H5' H H5' N N N 0 -2.508 -0.939 1.492
17 H6 H H6 N N N 0 1.812 0.236 2.227
18 H6' H H6' N N N 0 -4.116 -2.205 0.035
19 H6'A H H6'A N N N 0 -2.836 -2.351 -1.193
20 H7 H H7 N N N 0 5.452 -0.083 1.477
21 H7A H H7A N N N 0 4.417 1.007 2.43
22 H7B H H7B N N N 0 4.312 -0.754 2.668
23 HN3 H HN3 N N N 0 3.026 -0.456 -2.349
24 HO2' H HO2' N N N 0 -0.468 3.39 0.098
25 HO3' H HO3' N N N 0 -3.832 2.773 -0.228
26 HO4' H HO4' N N N 0 -4.894 1.043 -0.242
27 HO6' H HO6' N N N 0 -2.884 -4.238 0.27
28 N1 N N1 N N N 0 1.148 0.0040 0.22
29 N3 N N3 N N N 0 2.791 -0.316 -1.418
30 O2 O O2 N N N 0 0.634 -0.261 -1.917
31 O2' O O2' N N N 0 -0.157 2.549 0.46
32 O3' O O3' N N N 0 -2.886 2.648 -0.39
33 O4 O O4 N N N 0 4.93 -0.36 -0.803
34 O4' O O4' N N N 0 -4.417 0.288 0.128
35 O5' O O5' N N N 0 -0.987 -1.001 0.094
36 O6' O O6' N N N 0 -2.51 -3.395 0.559



CKB : 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 C2 N1 C N sing 1.35 N N
2 C2 N3 C N sing 1.35 N N
3 C2 O2 C O doub 1.22 N N
4 C4 C5 C C sing 1.42 N N
5 C4 N3 C N sing 1.35 N N
6 C4 O4 C O doub 1.22 N N
7 C5 C6 C C doub 1.35 N N
8 C5 C7 C C sing 1.51 N N
9 C6 N1 C N sing 1.37 N N
10 N1 C1' N C sing 1.46 N N
11 C1' C2' C C sing 1.53 N N
12 C1' O5' C O sing 1.43 N N
13 C2' C3' C C sing 1.53 N N
14 C2' O2' C O sing 1.43 N N
15 C3' C4' C C sing 1.53 N N
16 C3' O3' C O sing 1.43 N N
17 C4' C5' C C sing 1.53 N N
18 C4' O4' C O sing 1.43 N N
19 C5' C6' C C sing 1.53 N N
20 C5' O5' C O sing 1.43 N N
21 C6' O6' C O sing 1.43 N N
22 C6 H6 C H sing 1.08 N N
23 C7 H7 C H sing 1.09 N N
24 C7 H7A C H sing 1.09 N N
25 C7 H7B C H sing 1.09 N N
26 N3 HN3 N H sing 0.97 N N
27 C1' H1' C H sing 1.09 N N
28 C2' H2' C H sing 1.09 N N
29 C3' H3' C H sing 1.09 N N
30 C4' H4' C H sing 1.09 N N
31 C5' H5' C H sing 1.09 N N
32 C6' H6' C H sing 1.09 N N
33 C6' H6'A C H sing 1.09 N N
34 O6' HO6' O H sing 0.97 N N
35 O2' HO2' O H sing 0.97 N N
36 O3' HO3' O H sing 0.97 N N
37 O4' HO4' O H sing 0.97 N N



CKB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
CKB 3bd7 Open in New Window Bound ligand 2 1