Chemical Components in the PDB

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TS1 : Summary

Code

TS1

One-letter code

X

Molecule name

4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-deoxy-1-{2,6,8-trioxo-7-[4-(phosphonooxy)butyl]-1,2,3,6,7,8-hexahydro-9H-purin-9-yl}-D-arabinitol
OpenEye OEToolkits 1.5.0 4-[2,6,8-trioxo-9-[(2R,3S,4R)-2,3,4,5-tetrahydroxypentyl]-3H-purin-7-yl]butyl dihydrogen phosphate

Formula

C14 H23 N4 O11 P

Formal charge

0

Molecular weight

454.326 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C2=C(NC(=O)N1)N(C(=O)N2CCCCOP(=O)(O)O)CC(O)C(O)C(O)CO
SMILES CACTVS 3.341 OC[CH](O)[CH](O)[CH](O)CN1C(=O)N(CCCCO[P](O)(O)=O)C2=C1NC(=O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C(CCOP(=O)(O)O)CN1C2=C(NC(=O)NC2=O)N(C1=O)CC(C(C(CO)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@@H](O)[C@@H](O)[C@H](O)CN1C(=O)N(CCCCO[P](O)(O)=O)C2=C1NC(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C(CCOP(=O)(O)O)CN1C2=C(NC(=O)NC2=O)N(C1=O)C[C@H]([C@@H]([C@@H](CO)O)O)O

IUPAC InChI

InChI=1S/C14H23N4O11P/c19-6-8(21)10(22)7(20)5-18-11-9(12(23)16-13(24)15-11)17(14(18)25)3-1-2-4-29-30(26,27)28/h7-8,10,19-22H,1-6H2,(H2,26,27,28)(H2,15,16,23,24)/t7-,8-,10+/m1/s1

IUPAC InChI key

VBXZSBKAJFXURR-MRTMQBJTSA-N
TS1

wwPDB Information

Atom count

53 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-07-01

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



TS1 : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 4.707 0.758 2.327
2 C2 C C2 N Y N 0 3.729 0.403 1.696
3 N3 N N3 N Y N 0 3.897 -0.26 0.538
4 N1 N N1 N Y N 0 2.501 0.681 2.17
5 C8 C C8 N Y N 0 1.382 0.288 1.472
6 C9 C C9 N Y N 0 1.532 -0.387 0.292
7 C4 C C4 N Y N 0 2.83 -0.662 -0.183
8 O4 O O4 N N N 0 2.987 -1.263 -1.231
9 N7 N N7 N Y N 0 0.036 0.419 1.704
10 C10 C C10 N N N 0 -0.568 1.078 2.863
11 C11 C C11 R N N 0 -0.784 0.053 3.979
12 C12 C C12 S N N 0 -1.416 0.742 5.189
13 C13 C C13 R N N 0 -1.631 -0.282 6.305
14 C14 C C14 N N N 0 -2.264 0.406 7.516
15 O26 O O26 N N N 0 -2.465 -0.551 8.557
16 O23 O O23 N N N 0 -2.499 -1.318 5.839
17 O21 O O21 N N N 0 -0.548 1.777 5.655
18 O19 O O19 N N N 0 0.473 -0.512 4.355
19 C6 C C6 N Y N 0 -0.636 -0.153 0.688
20 O6 O O6 N N N 0 -1.847 -0.207 0.583
21 N5 N N5 N Y N 0 0.249 -0.657 -0.194
22 C15 C C15 N N N 0 -0.072 -1.36 -1.438
23 C16 C C16 N N N 0 -0.179 -0.35 -2.582
24 C17 C C17 N N N 0 -0.516 -1.084 -3.881
25 C18 C C18 N N N 0 -0.623 -0.073 -5.025
26 O27 O O27 N N N 0 -0.938 -0.759 -6.238
27 P P P N N N 0 -1.035 0.359 -7.393
28 O33 O O33 N N N 0 -1.389 -0.347 -8.796
29 O31 O O31 N N N 0 -2.188 1.418 -7.019
30 O32 O O32 N N N 0 0.261 1.062 -7.508
31 H3 H H3 N N N 0 4.793 -0.448 0.217
32 H1 H H1 N N N 0 2.403 1.161 3.008
33 H101 H 1H10 N N N 0 -1.527 1.51 2.576
34 H102 H 2H10 N N N 0 0.093 1.868 3.219
35 H11 H H11 N N N 0 -1.446 -0.736 3.623
36 H12 H H12 N N N 0 -2.375 1.173 4.902
37 H13 H H13 N N N 0 -0.672 -0.714 6.592
38 H141 H 1H14 N N N 0 -3.223 0.837 7.228
39 H142 H 2H14 N N N 0 -1.602 1.195 7.871
40 H26 H H26 N N N 0 -2.864 -0.077 9.299
41 H23 H H23 N N N 0 -3.334 -0.894 5.596
42 H21 H H21 N N N 0 0.286 1.354 5.899
43 H19 H H19 N N N 0 1.027 0.217 4.662
44 H151 H 1H15 N N N 0 0.713 -2.081 -1.663
45 H152 H 2H15 N N N 0 -1.022 -1.882 -1.325
46 H161 H 1H16 N N N 0 -0.966 0.37 -2.357
47 H162 H 2H16 N N N 0 0.77 0.172 -2.695
48 H171 H 1H17 N N N 0 0.269 -1.805 -4.106
49 H172 H 2H17 N N N 0 -1.466 -1.606 -3.768
50 H181 H 1H18 N N N 0 -1.409 0.647 -4.8
51 H182 H 2H18 N N N 0 0.326 0.448 -5.138
52 H33 H H33 N N N 0 -1.437 0.355 -9.458
53 H31 H H31 N N N 0 -3.015 0.919 -6.954



TS1 : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C2 O C doub 1.22 N N
2 C2 N3 C N sing 1.34 N Y
3 C2 N1 C N sing 1.35 N Y
4 N3 C4 N C sing 1.35 N Y
5 N3 H3 N H sing 0.97 N N
6 N1 C8 N C sing 1.38 N Y
7 N1 H1 N H sing 0.97 N N
8 C8 C9 C C doub 1.37 N Y
9 C8 N7 C N sing 1.37 N Y
10 C9 C4 C C sing 1.41 N Y
11 C9 N5 C N sing 1.4 N Y
12 C4 O4 C O doub 1.22 N N
13 N7 C10 N C sing 1.46 N N
14 N7 C6 N C sing 1.35 N Y
15 C10 C11 C C sing 1.53 N N
16 C10 H101 C H sing 1.09 N N
17 C10 H102 C H sing 1.09 N N
18 C11 C12 C C sing 1.53 N N
19 C11 O19 C O sing 1.43 N N
20 C11 H11 C H sing 1.09 N N
21 C12 C13 C C sing 1.53 N N
22 C12 O21 C O sing 1.43 N N
23 C12 H12 C H sing 1.09 N N
24 C13 C14 C C sing 1.53 N N
25 C13 O23 C O sing 1.43 N N
26 C13 H13 C H sing 1.09 N N
27 C14 O26 C O sing 1.43 N N
28 C14 H141 C H sing 1.09 N N
29 C14 H142 C H sing 1.09 N N
30 O26 H26 O H sing 0.97 N N
31 O23 H23 O H sing 0.97 N N
32 O21 H21 O H sing 0.97 N N
33 O19 H19 O H sing 0.97 N N
34 C6 O6 C O doub 1.22 N N
35 C6 N5 C N sing 1.35 N Y
36 N5 C15 N C sing 1.46 N N
37 C15 C16 C C sing 1.53 N N
38 C15 H151 C H sing 1.09 N N
39 C15 H152 C H sing 1.09 N N
40 C16 C17 C C sing 1.53 N N
41 C16 H161 C H sing 1.09 N N
42 C16 H162 C H sing 1.09 N N
43 C17 C18 C C sing 1.53 N N
44 C17 H171 C H sing 1.09 N N
45 C17 H172 C H sing 1.09 N N
46 C18 O27 C O sing 1.43 N N
47 C18 H181 C H sing 1.09 N N
48 C18 H182 C H sing 1.09 N N
49 O27 P O P sing 1.61 N N
50 P O33 P O sing 1.61 N N
51 P O31 P O sing 1.61 N N
52 P O32 P O doub 1.48 N N
53 O33 H33 O H sing 0.97 N N
54 O31 H31 O H sing 0.97 N N



TS1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TS1 1w29 Open in New Window Bound ligand 4 1