Chemical Components in the PDB

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T0T : Summary

Code

T0T

One-letter code

X

Molecule name

(1R)-1-{4-[(E)-2-(2-aminophenyl)ethenyl]phenyl}-1,4-anhydro-2-deoxy-5-O-phosphonato-D-erythro-pentitol

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R)-1-{4-[(E)-2-(2-aminophenyl)ethenyl]phenyl}-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
OpenEye OEToolkits 1.7.6 [(2R,3S,5R)-5-[4-[(E)-2-(2-aminophenyl)ethenyl]phenyl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C19 H22 N O6 P

Formal charge

0

Molecular weight

391.355 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(OCC3OC(c2ccc(\C=C\c1ccccc1N)cc2)CC3O)O
SMILES CACTVS 3.385 Nc1ccccc1C=Cc2ccc(cc2)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.7.6 c1ccc(c(c1)C=Cc2ccc(cc2)C3CC(C(O3)COP(=O)(O)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ccccc1/C=C/c2ccc(cc2)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(c(c1)/C=C/c2ccc(cc2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N

IUPAC InChI

InChI=1S/C19H22NO6P/c20-16-4-2-1-3-14(16)8-5-13-6-9-15(10-7-13)18-11-17(21)19(26-18)12-25-27(22,23)24/h1-10,17-19,21H,11-12,20H2,(H2,22,23,24)/b8-5+/t17-,18+,19+/m0/s1

IUPAC InChI key

NAVOUHWZGHPJBG-YOKLGZCWSA-N
T0T

wwPDB Information

Atom count

49 (27 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-06-24

Last modified at

2014-11-28

Status

Released

Obsoleted

Not Assigned



T0T : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -5.27 2.276 -0.221
2 C1 C C1 N Y N 0 -0.181 -1.94 -0.349
3 C2 C C2 N Y N 0 0.733 -2.846 -0.858
4 C3 C C3 N Y N 0 2.076 -2.535 -0.882
5 C4 C C4 N Y N 0 2.514 -1.302 -0.391
6 C5 C C5 N Y N 0 1.585 -0.392 0.121
7 C6 C C6 N Y N 0 0.244 -0.717 0.139
8 C7 C C7 N N N 0 3.948 -0.963 -0.413
9 C8 C C8 N N N 0 4.365 0.224 0.059
10 C9 C C9 N Y N 0 5.797 0.562 0.037
11 C1' C C1' R N N 0 -1.648 -2.285 -0.331
12 C10 C C10 N Y N 0 6.726 -0.346 -0.474
13 C11 C C11 N Y N 0 8.067 -0.022 -0.492
14 C12 C C12 N Y N 0 8.498 1.2 -0.004
15 C13 C C13 N Y N 0 7.59 2.109 0.505
16 C14 C C14 N Y N 0 6.237 1.804 0.525
17 N15 N N15 N N N 0 5.319 2.721 1.033
18 C2' C C2' N N N 0 -2.079 -2.764 1.079
19 C3' C C3' S N N 0 -3.595 -2.45 1.078
20 O3' O O3' N N N 0 -4.349 -3.621 0.76
21 C4' C C4' R N N 0 -3.76 -1.386 -0.025
22 O4' O O4' N N N 0 -2.451 -1.104 -0.546
23 C5' C C5' N N N 0 -4.37 -0.113 0.567
24 OP3 O OP3 N N N 0 -4.253 3.163 0.658
25 O5' O O5' N N N 0 -4.627 0.823 -0.481
26 OP1 O OP1 N N N 0 -5.537 3.005 -1.631
27 OP2 O OP2 N N N 0 -6.549 2.126 0.508
28 H2 H H2 N N N 0 0.393 -3.798 -1.237
29 H3 H H3 N N N 0 2.789 -3.243 -1.28
30 H5 H H5 N N N 0 1.916 0.563 0.502
31 H6 H H6 N N N 0 -0.475 -0.015 0.535
32 H7 H H7 N N N 0 4.663 -1.668 -0.81
33 H8 H H8 N N N 0 3.649 0.929 0.456
34 H1' H H1' N N N 0 -1.872 -3.045 -1.08
35 H10 H H10 N N N 0 6.396 -1.301 -0.855
36 H11 H H11 N N N 0 8.785 -0.726 -0.887
37 H12 H H12 N N N 0 9.549 1.444 -0.022
38 H13 H H13 N N N 0 7.934 3.06 0.884
39 HN15 H HN15 N N N 0 4.374 2.504 1.05
40 HN1A H HN1A N N N 0 5.626 3.578 1.369
41 H2' H H2' N N N 0 -1.904 -3.833 1.197
42 H2'A H H2'A N N N 0 -1.565 -2.198 1.856
43 H3' H H3' N N N 0 -3.902 -2.05 2.045
44 HO3' H HO3' N N N 0 -4.236 -4.345 1.391
45 H4' H H4' N N N 0 -4.4 -1.771 -0.819
46 H5' H H5' N N N 0 -5.305 -0.359 1.072
47 H5'A H H5'A N N N 0 -3.674 0.324 1.283
48 H21 H H21 N N N 0 -5.925 3.888 -1.55
49 H23 H H23 N N N 0 -3.392 3.303 0.241



T0T : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O5' P O sing 1.61 N N
2 P OP1 P O sing 1.61 N N
3 P OP2 P O doub 1.48 N N
4 P OP3 P O sing 1.61 N N
5 C1 C2 C C doub 1.38 N Y
6 C1 C6 C C sing 1.38 N Y
7 C1 C1' C C sing 1.51 N N
8 C2 C3 C C sing 1.38 N Y
9 C3 C4 C C doub 1.4 N Y
10 C4 C5 C C sing 1.4 N Y
11 C4 C7 C C sing 1.47 N N
12 C5 C6 C C doub 1.38 N Y
13 C7 C8 C C doub 1.34 E N
14 C8 C9 C C sing 1.47 N N
15 C9 C10 C C doub 1.4 N Y
16 C9 C14 C C sing 1.41 N Y
17 C1' C2' C C sing 1.55 N N
18 C1' O4' C O sing 1.44 N N
19 C10 C11 C C sing 1.38 N Y
20 C11 C12 C C doub 1.38 N Y
21 C12 C13 C C sing 1.38 N Y
22 C13 C14 C C doub 1.39 N Y
23 C14 N15 C N sing 1.39 N N
24 C2' C3' C C sing 1.55 N N
25 C3' O3' C O sing 1.43 N N
26 C3' C4' C C sing 1.54 N N
27 C4' O4' C O sing 1.44 N N
28 C4' C5' C C sing 1.53 N N
29 C5' O5' C O sing 1.43 N N
30 C2 H2 C H sing 1.08 N N
31 C3 H3 C H sing 1.08 N N
32 C5 H5 C H sing 1.08 N N
33 C6 H6 C H sing 1.08 N N
34 C7 H7 C H sing 1.08 N N
35 C8 H8 C H sing 1.08 N N
36 C1' H1' C H sing 1.09 N N
37 C10 H10 C H sing 1.08 N N
38 C11 H11 C H sing 1.08 N N
39 C12 H12 C H sing 1.08 N N
40 C13 H13 C H sing 1.08 N N
41 N15 HN15 N H sing 0.97 N N
42 N15 HN1A N H sing 0.97 N N
43 C2' H2' C H sing 1.09 N N
44 C2' H2'A C H sing 1.09 N N
45 C3' H3' C H sing 1.09 N N
46 O3' HO3' O H sing 0.97 N N
47 C4' H4' C H sing 1.09 N N
48 C5' H5' C H sing 1.09 N N
49 C5' H5'A C H sing 1.09 N N
50 OP1 H21 O H sing 0.97 N N
51 OP3 H23 O H sing 0.97 N N



T0T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
T0T 4uqg Open in New Window Polymer component 1 1