Chemical Components in the PDB

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T38 : Summary

Code

T38

One-letter code

T

Molecule name

2'-O-ETHOXYMETHYLENE THYMIDINE 5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-O-(ethoxymethyl)-5-methyluridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3R,4R,5R)-4-(ethoxymethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C13 H21 N2 O10 P

Formal charge

0

Molecular weight

396.287 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 P(=O)(O)(O)OCC1OC(C(C1O)OCOCC)N2C(=O)NC(=O)C(C)=C2
SMILES CACTVS 3.385 CCOCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O
SMILES OpenEye OEToolkits 1.7.6 CCOCOC1C(C(OC1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 CCOCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CCOCO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C13H21N2O10P/c1-3-22-6-23-10-9(16)8(5-24-26(19,20)21)25-12(10)15-4-7(2)11(17)14-13(15)18/h4,8-10,12,16H,3,5-6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1

IUPAC InChI key

ZHEHKUXUPODKJV-DNRKLUKYSA-N
T38

wwPDB Information

Atom count

47 (26 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DT

Defined at

1998-07-29

Last modified at

2018-03-14

Status

Released

Obsoleted

Not Assigned



T38 : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 1.002 -0.001 0.881
2 C2 C C2 N N N 0 1.811 -1.538 -0.82
3 C2' C C2' R N N 0 0.949 1.228 -0.062
4 C3' C C3' R N N 0 -0.471 1.782 0.208
5 C4 C C4 N N N 0 3.753 -2.807 -0.549
6 C4' C C4' R N N 0 -1.237 0.585 0.805
7 C5 C C5 N N N 0 3.938 -2.231 0.73
8 C5' C C5' N N N 0 -2.458 0.266 -0.06
9 C5M C C5M N N N 0 5.12 -2.621 1.58
10 C6 C C6 N N N 0 3.045 -1.322 1.177
11 CA' C CA' N N N 0 2.338 3.045 -0.78
12 CB' C CB' N N N 0 1.261 5.053 -0.035
13 CD' C CD' N N N 0 0.133 6.026 -0.384
14 H1' H H1' N N N 0 1.242 0.306 1.899
15 H2' H H2' N N N 0 1.057 0.925 -1.103
16 H2P H H2P N N N 0 -5.924 0.121 0.776
17 H3 H H3 N N N 0 2.555 -2.833 -2.17
18 H3' H H3' N N N 0 -0.938 2.109 -0.721
19 H3P H H3P N N N 0 -5.896 -3.021 0.474
20 H4' H H4' N N N 0 -1.553 0.815 1.822
21 H5'1 H H5'1 N N N 0 -2.129 -0.056 -1.048
22 H5'2 H H5'2 N N N 0 -3.078 1.157 -0.155
23 H5M1 H H5M1 N N N 0 5.722 -3.358 1.048
24 H5M2 H H5M2 N N N 0 5.725 -1.739 1.789
25 H5M3 H H5M3 N N N 0 4.767 -3.05 2.518
26 H6 H H6 N N N 0 3.172 -0.868 2.148
27 HA H HA N N N 0 -1.285 3.207 1.395
28 HA'1 H HA'1 N N N 0 3.265 3.555 -0.518
29 HA'2 H HA'2 N N N 0 2.49 2.452 -1.681
30 HB'1 H HB'1 N N N 0 1.075 4.619 0.947
31 HB'2 H HB'2 N N N 0 2.211 5.587 -0.023
32 HD'1 H HD'1 N N N 0 0.318 6.46 -1.367
33 HD'2 H HD'2 N N N 0 -0.817 5.491 -0.397
34 HD'3 H HD'3 N N N 0 0.093 6.819 0.362
35 N1 N N1 N N N 0 1.975 -0.983 0.394
36 N3 N N3 N N N 0 2.689 -2.443 -1.292
37 O1P O O1P N N N 0 -4.308 -1.823 -1.468
38 O2 O O2 N N N 0 0.855 -1.219 -1.501
39 O2' O O2' N N N 0 1.947 2.187 0.294
40 O2P O O2P N N N 0 -5.701 -0.223 -0.1
41 O3' O O3' N N N 0 -0.418 2.859 1.146
42 O3P O O3P N N Y 0 -5.082 -2.614 0.8
43 O4 O O4 N N N 0 4.549 -3.625 -0.976
44 O4' O O4' N N N 0 -0.337 -0.536 0.813
45 O5' O O5' N N N 0 -3.216 -0.779 0.554
46 OC' O OC' N N N 0 1.312 4.013 -1.013
47 P P P N N N 0 -4.571 -1.37 -0.084



T38 : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O doub 1.48 N N
2 P O2P P O sing 1.61 N N
3 P O3P P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 O2P H2P O H sing 0.97 N N
6 O3P H3P O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5'1 C H sing 1.09 N N
10 C5' H5'2 C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.55 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HA O H sing 0.97 N N
19 C2' O2' C O sing 1.43 N N
20 C2' C1' C C sing 1.55 N N
21 C2' H2' C H sing 1.09 N N
22 O2' CA' O C sing 1.43 N N
23 C1' N1 C N sing 1.47 N N
24 C1' H1' C H sing 1.09 N N
25 N1 C2 N C sing 1.34 N N
26 N1 C6 N C sing 1.37 N N
27 C2 O2 C O doub 1.22 N N
28 C2 N3 C N sing 1.35 N N
29 N3 C4 N C sing 1.35 N N
30 N3 H3 N H sing 0.97 N N
31 C4 O4 C O doub 1.22 N N
32 C4 C5 C C sing 1.41 N N
33 C5 C5M C C sing 1.51 N N
34 C5 C6 C C doub 1.35 N N
35 C5M H5M1 C H sing 1.09 N N
36 C5M H5M2 C H sing 1.09 N N
37 C5M H5M3 C H sing 1.09 N N
38 C6 H6 C H sing 1.08 N N
39 CA' OC' C O sing 1.43 N N
40 CA' HA'1 C H sing 1.09 N N
41 CA' HA'2 C H sing 1.09 N N
42 CB' OC' C O sing 1.43 N N
43 CB' CD' C C sing 1.53 N N
44 CB' HB'1 C H sing 1.09 N N
45 CB' HB'2 C H sing 1.09 N N
46 CD' HD'1 C H sing 1.09 N N
47 CD' HD'2 C H sing 1.09 N N
48 CD' HD'3 C H sing 1.09 N N



T38 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
T38 410d Open in New Window Polymer component 2 1