Chemical Components in the PDB

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PBT : Summary

Code

PBT

One-letter code

N

Molecule name

[3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)-PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL DIHYDROGEN PHOSPHATE

Systematic names

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

Formula

C10 H17 N2 O8 P

Formal charge

0

Molecular weight

324.224 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N(CC(C(=O)N1)C)C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 C[CH]1CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 CC1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 C[C@@H]1CN([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 C[C@@H]1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H17N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h5-8,13H,2-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,7-,8-/m1/s1

IUPAC InChI key

PGRQANKWVMVANW-ULAWRXDQSA-N
PBT

wwPDB Information

Atom count

38 (21 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

Not Assigned

Defined at

2001-10-04

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PBT : Atoms of Molecule

Total Number of Atoms: 38
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 -3.968 -1.665 3.118
2 O1P O O1P N N N 0 -3.912 -2.311 1.636
3 O2P O O2P N N Y 0 -4.901 -0.36 2.92
4 O3P O O3P N N Y 0 -4.406 -2.599 4.208
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 2.326 -2.535 0.382
15 O2 O O2 N N N 0 3.415 -1.956 0.4
16 N3 N N3 N N N 0 2.173 -3.767 -0.267
17 C4 C C4 N N N 0 1.083 -4.633 -0.213
18 O4 O O4 N N N 0 1.03 -5.682 -0.852
19 C5 C C5 R N N 0 0.011 -4.203 0.774
20 C5M C C5M N N N 0 -1.324 -4.878 0.481
21 C6 C C6 N N N 0 -0.124 -2.687 0.747
22 H1P H H1P N N N 0 -4.684 -2.823 1.313
23 H2P H H2P N N N 0 -5.874 -0.475 2.871
24 H5'1 H 1H5* N N N 0 -1.971 -0.654 1.366
25 H5'2 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 HA H HA N N N 0 1.332 2.718 1.693
29 H2'1 H 1H2* N N N 0 -0.003 -0.001 0.003
30 H2'2 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 2.965 -4.08 -0.822
33 H5 H H5 N N N 0 0.354 -4.523 1.766
34 H5M1 H 1H5M N N N 0 -1.965 -4.861 1.367
35 H5M2 H 2H5M N N N 0 -1.845 -4.365 -0.332
36 H5M3 H 3H5M N N N 0 -1.17 -5.921 0.188
37 H6C1 H 1H6C N N N 0 -0.484 -2.336 -0.228
38 H6C2 H 2H6C N N N 0 -0.829 -2.358 1.519



PBT : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O sing 1.62 N N
2 P O2P P O sing 1.62 N N
3 P O3P P O doub 1.5 N N
4 P O5' P O sing 1.62 N N
5 O1P H1P O H sing 0.98 N N
6 O2P H2P 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' H5'1 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 1.52 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' HA O H sing 0.97 N N
19 C2' C1' C C sing 1.52 N N
20 C2' H2'1 C H sing 1.1 N N
21 C2' H2'2 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 1.4 N N
25 N1 C6 N C sing 1.46 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 1.52 N N
32 C5 C5M C C sing 1.52 N N
33 C5 C6 C C sing 1.52 N N
34 C5 H5 C H sing 1.1 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 H6C1 C H sing 1.1 N N
39 C6 H6C2 C H sing 1.1 N N



PBT : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
PBT 1ql5 Open in New Window Polymer component 2 2
PBT 2y1i Open in New Window Polymer component 1 1