Chemical Components in the PDB

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TDW : Summary

Code

TDW

One-letter code

X

Molecule name

2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(1S)-1-oxidanylethyl]-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(1S)-1-hydroxyethyl]-4-methyl-1,3lambda~5~-thiazol-5-yl}ethyl trihydrogen diphosphate
OpenEye OEToolkits 1.7.6 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(1S)-1-oxidanylethyl]-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate

Formula

C14 H23 N4 O8 P2 S

Formal charge

1

Molecular weight

469.367 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OCCc1sc(C(O)C)n(c1C)Cc2cnc(nc2N)C
SMILES CACTVS 3.370 C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
SMILES OpenEye OEToolkits 1.7.6 Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.370 C[C@H](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](C)O)CCOP(=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C14H24N4O8P2S/c1-8-12(4-5-25-28(23,24)26-27(20,21)22)29-14(9(2)19)18(8)7-11-6-16-10(3)17-13(11)15/h6,9,18-19H,4-5,7H2,1-3H3,(H,23,24)(H2,15,16,17)(H2,20,21,22)/t9-/m0/s1

IUPAC InChI key

WHPLAPKWYDKPQH-VIFPVBQESA-N
TDW

wwPDB Information

Atom count

52 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-08

Last modified at

2013-11-08

Status

Released

Obsoleted

Not Assigned



TDW : Atoms of Molecule

Total Number of Atoms: 52
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 S1 S S1 N Y N 0 1.374 1.969 -0.97
2 C2 C C2 N Y N 0 2.774 1.661 -0.038
3 N3 N N3 N Y N 1 2.692 0.499 0.517
4 C4 C C4 N Y N 0 1.604 -0.205 0.28
5 C5 C C5 N Y N 0 0.718 0.397 -0.519
6 C6 C C6 N N N 0 -0.608 -0.169 -0.958
7 C7 C C7 N N N 0 -1.692 0.234 0.044
8 O7 O O7 N N N 0 -2.949 -0.303 -0.372
9 PA P PA N N N 0 -4.315 -0.075 0.449
10 PB P PB N N N 0 -7.141 -0.484 -0.344
11 N1' N N1' N Y N 0 5.51 -1.529 -1.544
12 O1A O O1A N N N 0 -4.54 1.375 0.64
13 O1B O O1B N N N 0 -7.796 -1.119 -1.67
14 C2' C C2' N Y N 0 6.617 -1.972 -0.984
15 C27 C C27 S N N 0 3.935 2.609 0.113
16 O28 O O28 N N N 0 4.283 3.144 -1.166
17 C29 C C29 N N N 0 3.544 3.75 1.054
18 O2A O O2A N N N 0 -4.204 -0.794 1.885
19 O2B O O2B N N N 0 -7.76 -1.203 0.957
20 N3' N N3' N Y N 0 6.855 -1.818 0.303
21 O3A O O3A N N N 0 -5.547 -0.706 -0.373
22 O3B O O3B N N N 0 -7.437 0.966 -0.294
23 C4' C C4' N Y N 0 5.975 -1.202 1.087
24 N4' N N4' N N N 0 6.228 -1.042 2.44
25 C5' C C5' N Y N 0 4.791 -0.72 0.525
26 C6' C C6' N Y N 0 4.584 -0.905 -0.828
27 C7' C C7' N N N 0 3.764 -0.016 1.374
28 CM2 C CM2 N N N 0 7.639 -2.675 -1.839
29 CM4 C CM4 N N N 0 1.377 -1.576 0.863
30 H6 H H6 N N N 0 -0.861 0.221 -1.944
31 H6A H H6A N N N 0 -0.542 -1.257 -1.003
32 H7 H H7 N N N 0 -1.439 -0.156 1.03
33 H7A H H7A N N N 0 -1.758 1.321 0.089
34 HO1B H HO1B N N N 0 -8.757 -1.022 -1.72
35 H27 H H27 N N N 0 4.79 2.074 0.527
36 HO28 H HO28 N N N 0 5.024 3.764 -1.145
37 H29 H H29 N N N 0 4.384 4.436 1.163
38 H29A H H29A N N N 0 2.689 4.285 0.64
39 H29B H H29B N N N 0 3.279 3.342 2.029
40 HO2A H HO2A N N N 0 -4.056 -1.749 1.837
41 HO2B H HO2B N N N 0 -7.604 -2.156 0.991
42 HN4' H HN4' N N N 0 7.09 -1.297 2.805
43 HN4A H HN4A N N N 0 5.544 -0.674 3.021
44 H6' H H6' N N N 0 3.681 -0.545 -1.297
45 H7' H H7' N N N 0 4.236 0.812 1.903
46 H7'A H H7'A N N N 0 3.346 -0.717 2.096
47 HM2 H HM2 N N N 0 8.344 -1.945 -2.237
48 HM2A H HM2A N N N 0 8.177 -3.406 -1.235
49 HM2B H HM2B N N N 0 7.137 -3.183 -2.662
50 HM4 H HM4 N N N 0 0.876 -1.483 1.827
51 HM4A H HM4A N N N 0 0.754 -2.16 0.185
52 HM4B H HM4B N N N 0 2.335 -2.077 0.998



TDW : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 S1 C S sing 1.71 N Y
2 S1 C5 S C sing 1.76 N Y
3 C27 C2 C C sing 1.51 N N
4 C2 N3 C N doub 1.29 N Y
5 C7' N3 C N sing 1.47 N N
6 N3 C4 N C sing 1.32 N Y
7 C4 C5 C C doub 1.34 N Y
8 C4 CM4 C C sing 1.51 N N
9 C5 C6 C C sing 1.51 N N
10 C7 C6 C C sing 1.53 N N
11 C6 H6 C H sing 1.09 N N
12 C6 H6A C H sing 1.09 N N
13 C7 O7 C O sing 1.43 N N
14 C7 H7 C H sing 1.09 N N
15 C7 H7A C H sing 1.09 N N
16 O7 PA O P sing 1.61 N N
17 O3A PA O P sing 1.61 N N
18 O1A PA O P doub 1.48 N N
19 PA O2A P O sing 1.61 N N
20 O3B PB O P doub 1.48 N N
21 O2B PB O P sing 1.61 N N
22 PB O3A P O sing 1.61 N N
23 PB O1B P O sing 1.61 N N
24 C2' N1' C N doub 1.32 N Y
25 N1' C6' N C sing 1.33 N Y
26 O1B HO1B O H sing 0.97 N N
27 N3' C2' N C sing 1.32 N Y
28 CM2 C2' C C sing 1.51 N N
29 O28 C27 O C sing 1.43 N N
30 C27 C29 C C sing 1.53 N N
31 C27 H27 C H sing 1.09 N N
32 O28 HO28 O H sing 0.97 N N
33 C29 H29 C H sing 1.09 N N
34 C29 H29A C H sing 1.09 N N
35 C29 H29B C H sing 1.09 N N
36 O2A HO2A O H sing 0.97 N N
37 O2B HO2B O H sing 0.97 N N
38 N3' C4' N C doub 1.33 N Y
39 N4' C4' N C sing 1.39 N N
40 C4' C5' C C sing 1.4 N Y
41 N4' HN4' N H sing 0.97 N N
42 N4' HN4A N H sing 0.97 N N
43 C5' C7' C C sing 1.51 N N
44 C5' C6' C C doub 1.38 N Y
45 C6' H6' C H sing 1.08 N N
46 C7' H7' C H sing 1.09 N N
47 C7' H7'A C H sing 1.09 N N
48 CM2 HM2 C H sing 1.09 N N
49 CM2 HM2A C H sing 1.09 N N
50 CM2 HM2B C H sing 1.09 N N
51 CM4 HM4 C H sing 1.09 N N
52 CM4 HM4A C H sing 1.09 N N
53 CM4 HM4B C H sing 1.09 N N



TDW : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TDW 3zhv Open in New Window Bound ligand 4 1