Chemical Components in the PDB

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TPS : Summary

Code

TPS

One-letter code

X

Molecule name

THIAMIN PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazol-3-ium
OpenEye OEToolkits 1.5.0 2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl dihydrogen phosphate

Formula

C12 H18 N4 O4 P S

Formal charge

1

Molecular weight

345.334 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
SMILES CACTVS 3.341 Cc1ncc(C[n+]2csc(CCO[P](O)(O)=O)c2C)c(N)n1
SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)O
Canonical SMILES CACTVS 3.341 Cc1ncc(C[n+]2csc(CCO[P](O)(O)=O)c2C)c(N)n1
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)O

IUPAC InChI

InChI=1S/C12H17N4O4PS/c1-8-11(3-4-20-21(17,18)19)22-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H3-,13,14,15,17,18,19)/p+1

IUPAC InChI key

HZSAJDVWZRBGIF-UHFFFAOYSA-O
TPS

wwPDB Information

Atom count

40 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



TPS : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N Y N 0 1.362 -2.067 -0.278
2 C2A C C2A N Y N 0 5.526 1.307 0.606
3 C4 C C4 N Y N 0 0.392 -0.066 -0.347
4 C4A C C4A N Y N 0 4.525 -0.581 -0.247
5 C5 C C5 N Y N 0 -0.491 -0.635 0.48
6 C5A C C5A N Y N 0 3.541 0.221 -0.828
7 C6 C C6 N N N 0 -1.704 0.03 1.077
8 C6A C C6A N Y N 0 3.616 1.588 -0.645
9 C7 C C7 N N N 0 -2.903 -0.166 0.147
10 C7A C C7A N N N 0 2.424 -0.39 -1.635
11 CM2 C CM2 N N N 0 6.64 1.925 1.411
12 CM4 C CM4 N N N 0 0.278 1.367 -0.8
13 H2 H H2 N N N 0 2.1 -2.82 -0.512
14 H41N H H41N N N N 0 5.181 -2.507 0.0070
15 H42N H H42N N N N 0 3.784 -2.371 -0.916
16 H61 H H61 N N N 0 -1.921 -0.414 2.048
17 H62 H H62 N N N 0 -1.51 1.096 1.2
18 H6A H H6A N N N 0 2.872 2.239 -1.08
19 H71 H H71 N N N 0 -2.685 0.278 -0.825
20 H72 H H72 N N N 0 -3.096 -1.232 0.023
21 H7A1 H H7A1 N N N 0 2.81 -1.23 -2.212
22 H7A2 H H7A2 N N N 0 2.015 0.359 -2.314
23 HM21 H HM21 N N N 0 6.339 1.992 2.457
24 HM22 H HM22 N N N 0 7.534 1.306 1.33
25 HM23 H HM23 N N N 0 6.853 2.923 1.03
26 HM41 H HM41 N N N 0 -0.392 1.425 -1.658
27 HM42 H HM42 N N N 0 -0.121 1.974 0.013
28 HM43 H HM43 N N N 0 1.263 1.739 -1.082
29 HO2 H HO2 N N N 0 -7.474 1.173 0.609
30 HO3 H HO3 N N N 0 -5.159 2.207 -1.272
31 N1A N N1A N Y N 0 4.613 2.09 0.071
32 N3 N N3 N Y N 1 1.37 -0.86 -0.733
33 N3A N N3A N Y N 0 5.493 -0.0020 0.458
34 N4A N N4A N N N 0 4.494 -1.957 -0.401
35 O1 O O1 N N N 0 -5.901 -0.938 -0.281
36 O2 O O2 N N N 0 -6.58 1.143 0.974
37 O3 O O3 N N N 0 -5.418 1.282 -1.38
38 O7 O O7 N N N 0 -4.053 0.465 0.712
39 P1 P P1 N N N 0 -5.497 0.457 0.0
40 S1 S S1 N Y N 0 0.015 -2.302 0.748



TPS : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CM2 C2A C C sing 1.51 N N
2 CM2 HM21 C H sing 1.09 N N
3 CM2 HM22 C H sing 1.09 N N
4 CM2 HM23 C H sing 1.09 N N
5 N3 C2 N C doub 1.29 N Y
6 N3 C4 N C sing 1.32 N Y
7 N3 C7A N C sing 1.46 N N
8 C2 S1 C S sing 1.71 N Y
9 C2 H2 C H sing 1.08 N N
10 S1 C5 S C sing 1.76 N Y
11 C5 C4 C C doub 1.34 N Y
12 C5 C6 C C sing 1.51 N N
13 C4 CM4 C C sing 1.51 N N
14 CM4 HM41 C H sing 1.09 N N
15 CM4 HM42 C H sing 1.09 N N
16 CM4 HM43 C H sing 1.09 N N
17 C6 C7 C C sing 1.53 N N
18 C6 H61 C H sing 1.09 N N
19 C6 H62 C H sing 1.09 N N
20 C7 O7 C O sing 1.43 N N
21 C7 H71 C H sing 1.09 N N
22 C7 H72 C H sing 1.09 N N
23 O7 P1 O P sing 1.61 N N
24 N1A C2A N C doub 1.32 N Y
25 N1A C6A N C sing 1.33 N Y
26 C2A N3A C N sing 1.32 N Y
27 N3A C4A N C doub 1.33 N Y
28 C4A N4A C N sing 1.38 N N
29 C4A C5A C C sing 1.4 N Y
30 N4A H41N N H sing 0.97 N N
31 N4A H42N N H sing 0.97 N N
32 C5A C6A C C doub 1.38 N Y
33 C5A C7A C C sing 1.51 N N
34 C6A H6A C H sing 1.08 N N
35 C7A H7A1 C H sing 1.09 N N
36 C7A H7A2 C H sing 1.09 N N
37 P1 O1 P O doub 1.48 N N
38 P1 O2 P O sing 1.61 N N
39 P1 O3 P O sing 1.61 N N
40 O2 HO2 O H sing 0.97 N N
41 O3 HO3 O H sing 0.97 N N



TPS : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
TPS 1g4s Open in New Window Bound ligand 2 1
TPS 2hom Open in New Window Bound ligand 1 1
TPS 2qry Open in New Window Bound ligand 4 1
TPS 2tps Open in New Window Bound ligand 2 1
TPS 2y6z Open in New Window Bound ligand 1 1
TPS 3c9t Open in New Window Bound ligand 2 1
TPS 3nl3 Open in New Window Bound ligand 6 1
TPS 3nl6 Open in New Window Bound ligand 3 1
TPS 3nm3 Open in New Window Bound ligand 6 1
TPS 5dd7 Open in New Window Bound ligand 2 1
TPS 6fhh Open in New Window Polymer component 3 3