Chemical Components in the PDB

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UGB : Summary

Code

UGB

One-letter code

X

Molecule name

(2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S,3R,4S,5R,6R)-6-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid
OpenEye OEToolkits 1.7.0 (2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid

Formula

C15 H22 N2 O18 P2

Formal charge

0

Molecular weight

580.285 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(=O)O)C(O)C(O)C3O)O)O
SMILES CACTVS 3.370 O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
SMILES OpenEye OEToolkits 1.7.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
Canonical SMILES CACTVS 3.370 O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@@H]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
Canonical SMILES OpenEye OEToolkits 1.7.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)C(=O)O)O)O)O)O)O

IUPAC InChI

InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8-,9-,10-,11+,12-,14-/m1/s1

IUPAC InChI key

HDYANYHVCAPMJV-GXNRKQDOSA-N
UGB

wwPDB Information

Atom count

59 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-08-24

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



UGB : Atoms of Molecule

Total Number of Atoms: 59
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 5.66 -1.138 0.278
2 C2 C C2 N N N 0 6.22 -2.107 1.025
3 O2 O O2 N N N 0 6.269 -1.98 2.233
4 N3 N N3 N N N 0 6.724 -3.217 0.453
5 C4 C C4 N N N 0 6.676 -3.373 -0.885
6 O4 O O4 N N N 0 7.132 -4.377 -1.403
7 C5 C C5 N N N 0 6.091 -2.361 -1.683
8 C6 C C6 N N N 0 5.592 -1.258 -1.083
9 PA P PA N N N 0 0.059 1.973 -1.239
10 PB P PB N N N 0 -2.832 1.335 -1.09
11 O'P O O'P N N N 0 -6.625 -2.539 -1.777
12 O'Q O O'Q N N N 0 -5.51 -4.081 -0.653
13 C1' C C1' R N N 0 -5.124 0.69 0.122
14 O1A O O1A N N N 0 0.434 1.509 -2.735
15 O1B O O1B N N N 0 -3.144 0.608 -2.492
16 C1D C C1D R N N 0 5.114 0.056 0.929
17 C2' C C2' R N N 0 -5.592 0.649 1.579
18 O2' O O2' N N N 0 -5.011 1.738 2.298
19 O2A O O2A N N N 0 -0.192 3.431 -1.224
20 O2B O O2B N N N 0 -3.19 2.768 -1.186
21 C2D C C2D R N N 0 5.882 1.324 0.477
22 O2D O O2D N N N 0 7.041 1.534 1.286
23 C3' C C3' S N N 0 -5.152 -0.675 2.211
24 O3' O O3' N N N 0 -5.647 -0.754 3.549
25 O3A O O3A N N N 0 -1.264 1.196 -0.751
26 O3B O O3B N N N 0 -3.697 0.643 0.078
27 C3D C C3D S N N 0 4.834 2.439 0.713
28 O3D O O3D N N N 0 5.068 3.088 1.964
29 C4' C C4' R N N 0 -5.716 -1.835 1.386
30 O4' O O4' N N N 0 -7.144 -1.8 1.428
31 C4D C C4D R N N 0 3.486 1.691 0.737
32 O4D O O4D N N N 0 3.761 0.301 0.488
33 C5' C C5' S N N 0 -5.244 -1.698 -0.063
34 O5' O O5' N N N 0 -5.66 -0.433 -0.581
35 C5D C C5D N N N 0 2.565 2.244 -0.353
36 O5D O O5D N N N 0 1.28 1.628 -0.248
37 C6' C C6' N N N 0 -5.844 -2.803 -0.894
38 H5 H H5 N N N 0 6.043 -2.468 -2.756
39 H6 H H6 N N N 0 5.141 -0.476 -1.675
40 HO'Q H HO'Q N N N 0 -5.92 -4.754 -1.212
41 H1' H H1' N N N 0 -5.472 1.611 -0.346
42 HO1A H HO1A N N N 0 0.611 0.562 -2.82
43 HO1B H HO1B N N N 0 -2.933 -0.336 -2.502
44 H1D H H1D N N N 0 5.151 -0.049 2.013
45 H2' H H2' N N N 0 -6.679 0.727 1.615
46 HO2' H HO2' N N N 0 -5.244 2.609 1.948
47 H2D H H2D N N N 0 6.152 1.26 -0.577
48 HO2D H HO2D N N N 0 7.554 2.316 1.041
49 H3' H H3' N N N 0 -4.063 -0.729 2.222
50 HO3' H HO3' N N N 0 -5.334 -0.044 4.127
51 H3D H H3D N N N 0 4.857 3.162 -0.102
52 HO3D H HO3D N N N 0 5.928 3.526 2.025
53 H4' H H4' N N N 0 -5.363 -2.781 1.798
54 HO4' H HO4' N N N 0 -7.57 -2.508 0.926
55 H4D H H4D N N N 0 3.017 1.804 1.714
56 H5' H H5' N N N 0 -4.156 -1.765 -0.099
57 H5D H H5D N N N 0 2.462 3.322 -0.229
58 H5DA H H5DA N N N 0 2.993 2.03 -1.332
59 HN3 H HN3 N N N 0 7.124 -3.906 1.007



UGB : Chemical Bonds

Total Number of Bonds: 61
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1D N1 C N sing 1.47 N N
2 C6 N1 C N sing 1.37 N N
3 N1 C2 N C sing 1.35 N N
4 C2 O2 C O doub 1.22 N N
5 C2 N3 C N sing 1.35 N N
6 C4 N3 C N sing 1.35 N N
7 C5 C4 C C sing 1.42 N N
8 C4 O4 C O doub 1.22 N N
9 C6 C5 C C doub 1.35 N N
10 C5 H5 C H sing 1.08 N N
11 C6 H6 C H sing 1.08 N N
12 O2A PA O P doub 1.48 N N
13 O3A PA O P sing 1.61 N N
14 PA O1A P O sing 1.61 N N
15 PA O5D P O sing 1.61 N N
16 O2B PB O P doub 1.48 N N
17 O3A PB O P sing 1.61 N N
18 O3B PB O P sing 1.61 N N
19 PB O1B P O sing 1.61 N N
20 O'P C6' O C doub 1.21 N N
21 C6' O'Q C O sing 1.34 N N
22 O'Q HO'Q O H sing 0.97 N N
23 O3B C1' O C sing 1.43 N N
24 O5' C1' O C sing 1.43 N N
25 C1' C2' C C sing 1.53 N N
26 C1' H1' C H sing 1.09 N N
27 O1A HO1A O H sing 0.97 N N
28 O1B HO1B O H sing 0.97 N N
29 C2D C1D C C sing 1.55 N N
30 O4D C1D O C sing 1.44 N N
31 C1D H1D C H sing 1.09 N N
32 C3' C2' C C sing 1.53 N N
33 C2' O2' C O sing 1.43 N N
34 C2' H2' C H sing 1.09 N N
35 O2' HO2' O H sing 0.97 N N
36 C3D C2D C C sing 1.55 N N
37 C2D O2D C O sing 1.43 N N
38 C2D H2D C H sing 1.09 N N
39 O2D HO2D O H sing 0.97 N N
40 C4' C3' C C sing 1.53 N N
41 C3' O3' C O sing 1.43 N N
42 C3' H3' C H sing 1.09 N N
43 O3' HO3' O H sing 0.97 N N
44 C3D O3D C O sing 1.43 N N
45 C3D C4D C C sing 1.54 N N
46 C3D H3D C H sing 1.09 N N
47 O3D HO3D O H sing 0.97 N N
48 C5' C4' C C sing 1.53 N N
49 C4' O4' C O sing 1.43 N N
50 C4' H4' C H sing 1.09 N N
51 O4' HO4' O H sing 0.97 N N
52 C5D C4D C C sing 1.53 N N
53 C4D O4D C O sing 1.44 N N
54 C4D H4D C H sing 1.09 N N
55 C6' C5' C C sing 1.51 N N
56 C5' O5' C O sing 1.43 N N
57 C5' H5' C H sing 1.09 N N
58 O5D C5D O C sing 1.43 N N
59 C5D H5D C H sing 1.09 N N
60 C5D H5DA C H sing 1.09 N N
61 N3 HN3 N H sing 0.97 N N



UGB : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
UGB 3oh1 Open in New Window Bound ligand 1 1
UGB 6zlk Open in New Window Bound ligand 4 1
UGB 6zll Open in New Window Bound ligand 4 1