Chemical Components in the PDB

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EOW : Summary

Code

EOW

One-letter code

X

Molecule name

(6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate

Formula

C11 H14 N O5 P

Formal charge

0

Molecular weight

271.206 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1c(O)c(CCC#C)ncc1CO[P](O)(O)=O
SMILES OpenEye OEToolkits 2.0.6 Cc1c(cnc(c1O)CCC#C)COP(=O)(O)O
Canonical SMILES CACTVS 3.385 Cc1c(O)c(CCC#C)ncc1CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1c(cnc(c1O)CCC#C)COP(=O)(O)O

IUPAC InChI

InChI=1S/C11H14NO5P/c1-3-4-5-10-11(13)8(2)9(6-12-10)7-17-18(14,15)16/h1,6,13H,4-5,7H2,2H3,(H2,14,15,16)

IUPAC InChI key

HYSIPFHNUDKCJU-UHFFFAOYSA-N
EOW

wwPDB Information

Atom count

32 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-04-05

Last modified at

2018-05-25

Status

Released

Obsoleted

Not Assigned



EOW : Atoms of Molecule

Total Number of Atoms: 32
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3P O O1 N N N 0 -4.721 -0.395 -1.061
2 P P P1 N N N 0 -4.044 0.478 0.111
3 O1P O O2 N N N 0 -4.543 2.005 -0.001
4 O2P O O3 N N N 0 -4.437 -0.074 1.427
5 O4P O O4 N N N 0 -2.442 0.424 -0.037
6 C5A C C1 N N N 0 -1.686 -0.778 0.121
7 C5 C C2 N Y N 0 -0.222 -0.481 -0.081
8 C6 C C3 N Y N 0 0.197 0.805 -0.366
9 N1 N N1 N Y N 0 1.475 1.076 -0.545
10 C4 C C4 N Y N 0 0.719 -1.492 0.022
11 C4A C C5 N N N 0 0.302 -2.905 0.337
12 C3 C C6 N Y N 0 2.059 -1.171 -0.172
13 O3 O O5 N N N 0 3.018 -2.129 -0.08
14 C2 C C7 N Y N 0 2.402 0.142 -0.461
15 C2A C C8 N N N 0 3.849 0.505 -0.674
16 C1 C C9 N N N 0 4.479 0.896 0.664
17 C7 C C10 N N N 0 5.892 1.25 0.456
18 C8 C C11 N N N 0 7.02 1.533 0.29
19 H1 H H1 N N N 0 -4.507 -0.089 -1.953
20 H2 H H2 N N N 0 -5.5 2.113 0.079
21 H3 H H3 N N N 0 -1.84 -1.174 1.125
22 H4 H H4 N N N 0 -2.013 -1.512 -0.614
23 H8 H H8 N N N 0 -0.6 -2.89 0.949
24 H5 H H5 N N N 0 -0.531 1.599 -0.444
25 H6 H H6 N N N 0 0.103 -3.441 -0.591
26 H7 H H7 N N N 0 1.102 -3.407 0.882
27 H9 H H9 N N N 0 3.21 -2.574 -0.917
28 H10 H H10 N N N 0 4.38 -0.351 -1.09
29 H11 H H11 N N N 0 3.914 1.345 -1.365
30 H12 H H12 N N N 0 3.947 1.751 1.081
31 H13 H H13 N N N 0 4.413 0.056 1.356
32 H14 H H14 N N N 0 8.028 1.786 0.141



EOW : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2P P O P doub 1.48 N N
2 C6 N1 C N doub 1.32 N Y
3 C6 C5 C C sing 1.38 N Y
4 N1 C2 N C sing 1.32 N Y
5 P O3P P O sing 1.61 N N
6 P O4P P O sing 1.61 N N
7 P O1P P O sing 1.61 N N
8 C5A O4P C O sing 1.43 N N
9 C5A C5 C C sing 1.51 N N
10 C5 C4 C C doub 1.38 N Y
11 C2 C2A C C sing 1.51 N N
12 C2 C3 C C doub 1.39 N Y
13 C2A C1 C C sing 1.53 N N
14 C1 C7 C C sing 1.47 N N
15 C4 C3 C C sing 1.39 N Y
16 C4 C4A C C sing 1.51 N N
17 C3 O3 C O sing 1.36 N N
18 C7 C8 C C trip 1.17 N N
19 O3P H1 O H sing 0.97 N N
20 O1P H2 O H sing 0.97 N N
21 C5A H3 C H sing 1.09 N N
22 C5A H4 C H sing 1.09 N N
23 C6 H5 C H sing 1.08 N N
24 C4A H6 C H sing 1.09 N N
25 C4A H7 C H sing 1.09 N N
26 C4A H8 C H sing 1.09 N N
27 O3 H9 O H sing 0.97 N N
28 C2A H10 C H sing 1.09 N N
29 C2A H11 C H sing 1.09 N N
30 C1 H12 C H sing 1.09 N N
31 C1 H13 C H sing 1.09 N N
32 C8 H14 C H sing 1.05 N N



EOW : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EOW 6g58 Open in New Window Bound ligand 2 1