Chemical Components in the PDB

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T3Q : Summary

Code

T3Q

One-letter code

X

Molecule name

[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate

Synonyms

thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.5.0 [[(2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyl-oxan-2-yl]oxy-hydroxy-phosphoryl] [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate

Formula

C16 H27 N3 O14 P2

Formal charge

0

Molecular weight

547.345 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(N)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
SMILES CACTVS 3.341 C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](N)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
Canonical SMILES CACTVS 3.341 C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](N)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N)O

IUPAC InChI

InChI=1S/C16H27N3O14P2/c1-6-4-19(16(24)18-14(6)23)10-3-8(20)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)11(17)12(21)7(2)30-15/h4,7-13,15,20-22H,3,5,17H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t7-,8+,9-,10-,11+,12-,13-,15-/m1/s1

IUPAC InChI key

KVYJLJOGNUNRJK-HALQBZCBSA-N
T3Q

wwPDB Information

Atom count

62 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-02-02

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



T3Q : Atoms of Molecule

Total Number of Atoms: 62
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O4 O O4 N N N 0 -7.027 -3.605 1.645
2 C4 C C4 N N N 0 -6.48 -2.745 0.978
3 N3 N N3 N N N 0 -6.067 -1.598 1.554
4 C2 C C2 N N N 0 -5.463 -0.647 0.817
5 O2 O O2 N N N 0 -5.095 0.382 1.35
6 C5 C C5 N N N 0 -6.268 -2.942 -0.408
7 C5M C C5M N N N 0 -6.715 -4.216 -1.075
8 C6 C C6 N N N 0 -5.66 -1.972 -1.123
9 N1 N N1 N N N 0 -5.259 -0.82 -0.502
10 C1' C C1* R N N 0 -4.599 0.232 -1.278
11 O4' O O4* N N N 0 -3.338 0.588 -0.671
12 C2' C C2* N N N 0 -5.435 1.531 -1.243
13 C3' C C3* S N N 0 -4.378 2.656 -1.178
14 O3' O O3* N N N 0 -4.48 3.506 -2.323
15 C4' C C4* R N N 0 -3.029 1.903 -1.181
16 C5' C C5* N N N 0 -2.024 2.607 -0.266
17 O5' O O5* N N N 0 -0.772 1.921 -0.317
18 PA P PA S N N 0 0.518 2.388 0.526
19 O1A O O1A N N N 0 0.165 2.476 1.961
20 O2A O O2A N N N 0 1.007 3.83 0.004
21 O3A O O3A N N N 0 1.704 1.316 0.33
22 PB P PB S N N 0 3.037 0.959 1.159
23 O1B O O1B N N N 0 2.655 0.031 2.418
24 O2B O O2B N N N 0 3.667 2.209 1.641
25 O3B O O3B N N N 0 4.067 0.172 0.205
26 O4Q O O4Q N N N 0 5.243 -3.625 -1.757
27 C4Q C C4Q S N N 0 5.768 -2.636 -0.869
28 C6Q C C6Q N N N 0 4.851 -3.849 1.114
29 C5Q C C5Q R N N 0 4.863 -2.518 0.359
30 O5Q O O5Q N N N 0 5.358 -1.488 1.217
31 C3Q C C3Q S N N 0 5.824 -1.283 -1.586
32 N3Q N N3Q N N N 0 6.75 -1.367 -2.723
33 C2Q C C2Q R N N 0 6.314 -0.216 -0.603
34 O2Q O O2Q N N N 0 6.303 1.062 -1.24
35 C1Q C C1Q R N N 0 5.387 -0.192 0.616
36 HN3 H HN3 N N N 0 -6.206 -1.457 2.504
37 H5M H H5M N N N 0 -7.181 -4.869 -0.337
38 H5MA H H5MA N N N 0 -7.436 -3.983 -1.859
39 H5MB H H5MB N N N 0 -5.853 -4.72 -1.512
40 H6 H H6 N N N 0 -5.489 -2.105 -2.182
41 H1' H H1* N N N 0 -4.446 -0.096 -2.307
42 H2' H H2* N N N 0 -6.035 1.623 -2.148
43 H2'A H H2*A N N N 0 -6.071 1.552 -0.358
44 H3' H H3* N N N 0 -4.492 3.235 -0.262
45 H5'A H H5*A N N N 0 -2.4 2.603 0.757
46 HO3' H HO3* N N N 0 -5.332 3.957 -2.403
47 H4' H H4* N N N 0 -2.635 1.834 -2.196
48 H5' H H5* N N N 0 -1.888 3.636 -0.599
49 HO2A H HO2A N N N 0 1.255 3.847 -0.93
50 HO1B H HO1B N N N 0 2.236 -0.807 2.176
51 HO4Q H HO4Q N N N 0 5.177 -4.508 -1.367
52 H4Q H H4Q N N N 0 6.772 -2.924 -0.556
53 H5Q H H5Q N N N 0 3.849 -2.271 0.042
54 H6Q H H6Q N N N 0 5.864 -4.095 1.432
55 H6QA H H6QA N N N 0 4.206 -3.765 1.989
56 H6QB H H6QB N N N 0 4.474 -4.635 0.459
57 H3Q H H3Q N N N 0 4.829 -1.02 -1.945
58 HN3Q H HN3Q N N N 0 6.804 -0.486 -3.212
59 HN3A H HN3A N N N 0 7.665 -1.67 -2.422
60 H2Q H H2Q N N N 0 7.329 -0.455 -0.283
61 HO2Q H HO2Q N N N 0 6.602 1.787 -0.674
62 H1Q H H1Q N N N 0 5.755 0.536 1.339



T3Q : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O4 C4 O C doub 1.22 N N
2 N3 C4 N C sing 1.35 N N
3 C4 C5 C C sing 1.42 N N
4 N3 C2 N C sing 1.35 N N
5 N3 HN3 N H sing 0.97 N N
6 O2 C2 O C doub 1.22 N N
7 C2 N1 C N sing 1.35 N N
8 C5 C5M C C sing 1.51 N N
9 C5 C6 C C doub 1.35 N N
10 C5M H5M C H sing 1.09 N N
11 C5M H5MA C H sing 1.09 N N
12 C5M H5MB C H sing 1.09 N N
13 N1 C6 N C sing 1.37 N N
14 C6 H6 C H sing 1.08 N N
15 N1 C1' N C sing 1.46 N N
16 C1' O4' C O sing 1.44 N N
17 C1' C2' C C sing 1.55 N N
18 C1' H1' C H sing 1.09 N N
19 O4' C4' O C sing 1.44 N N
20 C2' C3' C C sing 1.55 N N
21 C2' H2' C H sing 1.09 N N
22 C2' H2'A C H sing 1.09 N N
23 C4' C3' C C sing 1.54 N N
24 C3' O3' C O sing 1.43 N N
25 C3' H3' C H sing 1.09 N N
26 O3' HO3' O H sing 0.97 N N
27 C4' C5' C C sing 1.53 N N
28 C4' H4' C H sing 1.09 N N
29 O5' C5' O C sing 1.43 N N
30 C5' H5' C H sing 1.09 N N
31 C5' H5'A C H sing 1.09 N N
32 O5' PA O P sing 1.61 N N
33 O1A PA O P doub 1.48 N N
34 O2A PA O P sing 1.61 N N
35 PA O3A P O sing 1.61 N N
36 O2A HO2A O H sing 0.97 N N
37 O3A PB O P sing 1.61 N N
38 O2B PB O P doub 1.48 N N
39 O1B PB O P sing 1.61 N N
40 PB O3B P O sing 1.61 N N
41 O1B HO1B O H sing 0.97 N N
42 O3B C1Q O C sing 1.43 N N
43 C4Q O4Q C O sing 1.43 N N
44 O4Q HO4Q O H sing 0.97 N N
45 C5Q C4Q C C sing 1.53 N N
46 C3Q C4Q C C sing 1.53 N N
47 C4Q H4Q C H sing 1.09 N N
48 O5Q C5Q O C sing 1.43 N N
49 C5Q C6Q C C sing 1.53 N N
50 C5Q H5Q C H sing 1.09 N N
51 C1Q O5Q C O sing 1.43 N N
52 C6Q H6Q C H sing 1.09 N N
53 C6Q H6QA C H sing 1.09 N N
54 C6Q H6QB C H sing 1.09 N N
55 C2Q C3Q C C sing 1.53 N N
56 C3Q N3Q C N sing 1.47 N N
57 C3Q H3Q C H sing 1.09 N N
58 N3Q HN3Q N H sing 1.01 N N
59 N3Q HN3A N H sing 1.01 N N
60 O2Q C2Q O C sing 1.43 N N
61 C1Q C2Q C C sing 1.53 N N
62 C2Q H2Q C H sing 1.09 N N
63 O2Q HO2Q O H sing 0.97 N N
64 C1Q H1Q C H sing 1.09 N N



T3Q : Used in PDB Entries

Total Number of PDB Entries: 12
Ligand Code PDB Entry ID Type Total Distinct
T3Q 3fsb Open in New Window Bound ligand 2 1
T3Q 3pfh Open in New Window Bound ligand 2 1
T3Q 3px2 Open in New Window Bound ligand 2 1
T3Q 3px3 Open in New Window Bound ligand 2 1
T3Q 4lxt Open in New Window Bound ligand 2 1
T3Q 4ly3 Open in New Window Bound ligand 1 1
T3Q 4xcz Open in New Window Bound ligand 2 1
T3Q 4xd1 Open in New Window Bound ligand 1 1
T3Q 5uim Open in New Window Bound ligand 3 1
T3Q 7n7c Open in New Window Bound ligand 2 1
T3Q 7s3u Open in New Window Bound ligand 1 1
T3Q 7s43 Open in New Window Bound ligand 1 1