Chemical Components in the PDB

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THV : Summary

Code

THV

One-letter code

X

Molecule name

C2-1-HYDROXY-3-METHYL-PROPYL-THIAMIN DIPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-1-hydroxy-2-methylpropan-1-ide
OpenEye OEToolkits 1.5.0 2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-2-(1-hydroxy-2-methyl-propyl)-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate

Formula

C16 H26 N4 O8 P2 S

Formal charge

0

Molecular weight

496.412 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OCCc1sc([C-](O)C(C)C)[n+](c1C)Cc2cnc(nc2N)C
SMILES CACTVS 3.341 CC(C)[C-](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](C(C)C)O)CCOP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 CC(C)[C-](O)c1sc(CCO[P@](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](C(C)C)O)CCO[P@@](=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C16H26N4O8P2S/c1-9(2)14(21)16-20(8-12-7-18-11(4)19-15(12)17)10(3)13(31-16)5-6-27-30(25,26)28-29(22,23)24/h7,9,21H,5-6,8H2,1-4H3,(H,25,26)(H2,17,18,19)(H2,22,23,24)

IUPAC InChI key

VBABUKBBNKNHAI-UHFFFAOYSA-N
THV

wwPDB Information

Atom count

57 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-11-30

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



THV : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2B O O2B N N N 0 8.437 0.61 -0.378
2 PB P PB N N N 0 6.968 0.426 0.257
3 O3B O O3B N N N 0 6.697 1.596 1.329
4 O1B O O1B N N N 0 6.883 -0.889 0.93
5 O3A O O3A N N N 0 5.865 0.503 -0.913
6 PA P PA R N N 0 4.494 -0.075 -0.298
7 O1A O O1A N N N 0 4.588 -1.678 -0.188
8 O2A O O2A N N N 0 4.276 0.5 1.049
9 O5G O O5G N N N 0 3.264 0.326 -1.257
10 C5B C C5B N N N 0 2.071 -0.109 -0.602
11 C5A C C5A N N N 0 0.858 0.243 -1.466
12 C5 C C5 N Y N 0 -0.4 -0.215 -0.776
13 C4 C C4 N Y N 0 -1.17 0.45 0.083
14 C4A C C4A N N N 0 -0.809 1.859 0.477
15 S1 S S1 N Y N 0 -1.237 -1.787 -0.903
16 C2 C C2 N Y N 0 -2.583 -1.443 0.22
17 C8 C C8 N N N -1 -3.602 -2.227 0.588
18 O9 O O9 N N N 0 -3.932 -2.343 1.904
19 C9 C C9 N N N 0 -4.386 -2.983 -0.455
20 C10 C C10 N N N 0 -3.449 -3.926 -1.213
21 C11 C C11 N N N 0 -5.487 -3.798 0.227
22 N3 N N3 N Y N 1 -2.289 -0.137 0.606
23 C35 C C35 N N N 0 -3.146 0.581 1.552
24 C5' C C5* N Y N 0 -4.107 1.459 0.793
25 C6' C C6* N Y N 0 -3.776 2.761 0.476
26 N1' N N1* N Y N 0 -4.647 3.505 -0.193
27 C2' C C2* N Y N 0 -5.817 3.019 -0.556
28 C2A C C2A N N N 0 -6.773 3.903 -1.315
29 N3' N N3* N Y N 0 -6.173 1.783 -0.275
30 C4' C C4* N Y N 0 -5.352 0.974 0.388
31 N4' N N4* N N N 0 -5.731 -0.326 0.682
32 H2B H H2B N N N 0 9.066 0.557 0.355
33 H3B H H3B N N N 0 6.762 2.434 0.85
34 H1A H H1A N N N 0 4.73 -2.012 -1.085
35 H5B1 H 1H5B N N N 0 1.985 0.388 0.364
36 H5B2 H 2H5B N N N 0 2.11 -1.188 -0.454
37 H5A1 H 1H5A N N N 0 0.944 -0.253 -2.433
38 H5A2 H 2H5A N N N 0 0.819 1.323 -1.614
39 H4A1 H 1H4A N N N 0 -1.283 2.561 -0.21
40 H4A2 H 2H4A N N N 0 -1.158 2.053 1.491
41 H4A3 H 3H4A N N N 0 0.273 1.983 0.434
42 H9 H H9 N N N 0 -3.268 -1.848 2.403
43 HA H HA N N N 0 -4.835 -2.277 -1.153
44 H101 H 1H10 N N N 0 -3.0 -4.631 -0.514
45 H102 H 2H10 N N N 0 -4.016 -4.472 -1.967
46 H103 H 3H10 N N N 0 -2.665 -3.345 -1.698
47 H111 H 1H11 N N N 0 -5.038 -4.503 0.926
48 H112 H 2H11 N N N 0 -6.155 -3.126 0.767
49 H113 H 3H11 N N N 0 -6.054 -4.344 -0.527
50 H351 H 1H35 N N N 0 -3.706 -0.137 2.152
51 H352 H 2H35 N N N 0 -2.529 1.197 2.205
52 H6' H H6* N N N 0 -2.821 3.17 0.769
53 H2A1 H 1H2A N N N 0 -6.595 3.796 -2.385
54 H2A2 H 2H2A N N N 0 -7.798 3.611 -1.086
55 H2A3 H 3H2A N N N 0 -6.617 4.942 -1.023
56 H4'1 H 1H4* N N N 0 -6.471 -0.735 0.207
57 H4'2 H 2H4* N N N 0 -5.255 -0.828 1.363



THV : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2B PB O P sing 1.61 N N
2 O2B H2B O H sing 0.97 N N
3 PB O3B P O sing 1.61 N N
4 PB O1B P O doub 1.48 N N
5 PB O3A P O sing 1.61 N N
6 O3B H3B O H sing 0.97 N N
7 O3A PA O P sing 1.61 N N
8 PA O1A P O sing 1.61 N N
9 PA O2A P O doub 1.48 N N
10 PA O5G P O sing 1.61 N N
11 O1A H1A O H sing 0.97 N N
12 O5G C5B O C sing 1.43 N N
13 C5B C5A C C sing 1.53 N N
14 C5B H5B1 C H sing 1.09 N N
15 C5B H5B2 C H sing 1.09 N N
16 C5A C5 C C sing 1.51 N N
17 C5A H5A1 C H sing 1.09 N N
18 C5A H5A2 C H sing 1.09 N N
19 C5 C4 C C doub 1.33 N Y
20 C5 S1 C S sing 1.79 N Y
21 C4 C4A C C sing 1.51 N N
22 C4 N3 C N sing 1.37 N Y
23 C4A H4A1 C H sing 1.09 N N
24 C4A H4A2 C H sing 1.09 N N
25 C4A H4A3 C H sing 1.09 N N
26 S1 C2 S C sing 1.79 N Y
27 C2 C8 C C sing 1.34 N N
28 C2 N3 C N doub 1.39 N Y
29 C8 O9 C O sing 1.36 N N
30 C8 C9 C C sing 1.51 N N
31 O9 H9 O H sing 0.97 N N
32 C9 C10 C C sing 1.53 N N
33 C9 C11 C C sing 1.53 N N
34 C9 HA C H sing 1.09 N N
35 C10 H101 C H sing 1.09 N N
36 C10 H102 C H sing 1.09 N N
37 C10 H103 C H sing 1.09 N N
38 C11 H111 C H sing 1.09 N N
39 C11 H112 C H sing 1.09 N N
40 C11 H113 C H sing 1.09 N N
41 N3 C35 N C sing 1.46 N N
42 C35 C5' C C sing 1.51 N N
43 C35 H351 C H sing 1.09 N N
44 C35 H352 C H sing 1.09 N N
45 C5' C6' C C doub 1.38 N Y
46 C5' C4' C C sing 1.4 N Y
47 C6' N1' C N sing 1.33 N Y
48 C6' H6' C H sing 1.08 N N
49 N1' C2' N C doub 1.32 N Y
50 C2' C2A C C sing 1.51 N N
51 C2' N3' C N sing 1.32 N Y
52 C2A H2A1 C H sing 1.09 N N
53 C2A H2A2 C H sing 1.09 N N
54 C2A H2A3 C H sing 1.09 N N
55 N3' C4' N C doub 1.33 N Y
56 C4' N4' C N sing 1.39 N N
57 N4' H4'1 N H sing 0.97 N N
58 N4' H4'2 N H sing 0.97 N N



THV : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
THV 2beu Open in New Window Bound ligand 1 1
THV 2j9f Open in New Window Bound ligand 2 1