Chemical Components in the PDB

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DT : Summary

Code

DT

One-letter code

T

Molecule name

THYMIDINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-thymidylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H15 N2 O8 P

Formal charge

0

Molecular weight

322.208 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1

IUPAC InChI key

GYOZYWVXFNDGLU-XLPZGREQSA-N
DT

wwPDB Information

Atom count

36 (21 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-12-05

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DT : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O O3P N N Y 0 -3.912 -2.311 1.636
2 P P P N N N 0 -3.968 -1.665 3.118
3 OP1 O O1P N N N 0 -4.406 -2.599 4.208
4 OP2 O O2P N N N 0 -4.901 -0.36 2.92
5 O5' O O5* N N N 0 -2.493 -1.028 3.315
6 C5' C C5* N N N 0 -2.005 -0.136 2.327
7 C4' C C4* R N N 0 -0.611 0.328 2.728
8 O4' O O4* N N N 0 0.247 -0.829 2.764
9 C3' C C3* S N N 0 0.008 1.286 1.72
10 O3' O O3* N N N 0 0.965 2.121 2.368
11 C2' C C2* N N N 0 0.71 0.36 0.754
12 C1' C C1* R N N 0 1.157 -0.778 1.657
13 N1 N N1 N N N 0 1.164 -2.047 0.989
14 C2 C C2 N N N 0 2.333 -2.544 0.374
15 O2 O O2 N N N 0 3.41 -1.945 0.363
16 N3 N N3 N N N 0 2.194 -3.793 -0.24
17 C4 C C4 N N N 0 1.047 -4.57 -0.3
18 O4 O O4 N N N 0 0.995 -5.663 -0.857
19 C5 C C5 N N N 0 -0.143 -3.98 0.369
20 C7 C C5M N N N 0 -1.42 -4.757 0.347
21 C6 C C6 N N N 0 -0.013 -2.784 0.958
22 HOP3 H 3HOP N N N 0 -4.684 -2.823 1.313
23 HOP2 H 2HOP N N N 0 -5.874 -0.475 2.871
24 H5' H 1H5* N N N 0 -1.971 -0.654 1.366
25 H5'' H 2H5* N N N 0 -2.683 0.718 2.254
26 H4' H H4* N N N 0 -0.644 0.753 3.736
27 H3' H H3* N N N 0 -0.722 1.941 1.236
28 HO3' H H3T N N Y 0 0.743 3.042 2.146
29 H2' H 1H2* N N N 0 -0.003 -0.001 0.003
30 H2'' H 2H2* N N N 0 1.556 0.818 0.232
31 H1' H H1* N N N 0 2.163 -0.604 2.054
32 H3 H H3 N N N 0 3.023 -4.171 -0.689
33 H71 H 1H5M N N N 0 -1.735 -4.916 -0.683
34 H6 H H6 N N N 0 -0.857 -2.318 1.458
35 H72 H 2H5M N N N 0 -2.195 -4.208 0.881
36 H73 H 3H5M N N N 0 -1.272 -5.721 0.833



DT : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.62 N N
2 OP3 HOP3 O H sing 0.98 N N
3 P OP1 P O doub 1.5 N N
4 P OP2 P O sing 1.62 N N
5 P O5' P O sing 1.62 N N
6 OP2 HOP2 O H sing 0.98 N N
7 O5' C5' O C sing 1.42 N N
8 C5' C4' C C sing 1.52 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'' C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.52 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.43 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.51 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' C1' C C sing 1.52 N N
20 C2' H2' C H sing 1.1 N N
21 C2' H2'' C H sing 1.09 N N
22 C1' N1 C N sing 1.43 N N
23 C1' H1' C H sing 1.1 N N
24 N1 C2 N C sing 1.41 N N
25 N1 C6 N C sing 1.39 N N
26 C2 O2 C O doub 1.23 N N
27 C2 N3 C N sing 1.4 N N
28 N3 C4 N C sing 1.39 N N
29 N3 H3 N H sing 1.02 N N
30 C4 O4 C O doub 1.23 N N
31 C4 C5 C C sing 1.49 N N
32 C5 C7 C C sing 1.49 N N
33 C5 C6 C C doub 1.34 N N
34 C7 H71 C H sing 1.09 N N
35 C7 H72 C H sing 1.09 N N
36 C7 H73 C H sing 1.09 N N
37 C6 H6 C H sing 1.09 N N



DT : Used in PDB Entries

Total Number of PDB Entries: 17
Ligand Code PDB Entry ID Type Total Distinct
DT 4e0p Open in New Window Bound ligand 1 1
DT 4e0y Open in New Window Bound ligand 1 1
DT 4e0z Open in New Window Bound ligand 1 1
DT 4e10 Open in New Window Bound ligand 1 1
DT 4g06 Open in New Window Bound ligand 2 1
DT 4kpy Open in New Window Bound ligand 2 1
DT 4kx3 Open in New Window Bound ligand 1 1
DT 4n76 Open in New Window Bound ligand 1 1
DT 4nca Open in New Window Bound ligand 2 1
DT 4ncb Open in New Window Bound ligand 2 1
DT 4s0n Open in New Window Bound ligand 2 1
DT 4ynq Open in New Window Bound ligand 1 1
DT 5cdm Open in New Window Bound ligand 1 1
DT 6z9t Open in New Window Bound ligand 2 1
DT 7csy Open in New Window Bound ligand 1 1
DT 7l4m Open in New Window Bound ligand 1 1
DT 7s01 Open in New Window Bound ligand 1 1