Chemical Components in the PDB

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P2H : Summary

Code

P2H

One-letter code

X

Molecule name

1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium

Systematic names

ProgramVersionName
ACDLabs 11.02 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium
OpenEye OEToolkits 1.6.1 [1-hydroxy-2-(3-phenylpyridin-1-ium-1-yl)-1-phosphono-ethyl]phosphonic acid

Formula

C13 H16 N O7 P2

Formal charge

1

Molecular weight

360.216 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=P(O)(O)C(O)(P(=O)(O)O)C[n+]2cccc(c1ccccc1)c2
SMILES CACTVS 3.352 OC(C[n+]1cccc(c1)c2ccccc2)([P](O)(O)=O)[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.0 c1ccc(cc1)c2ccc[n+](c2)CC(O)(P(=O)(O)O)P(=O)(O)O
Canonical SMILES CACTVS 3.352 OC(C[n+]1cccc(c1)c2ccccc2)([P](O)(O)=O)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 c1ccc(cc1)c2ccc[n+](c2)CC(O)(P(=O)(O)O)P(=O)(O)O

IUPAC InChI

InChI=1S/C13H15NO7P2/c15-13(22(16,17)18,23(19,20)21)10-14-8-4-7-12(9-14)11-5-2-1-3-6-11/h1-9,15H,10H2,(H3-,16,17,18,19,20,21)/p+1

IUPAC InChI key

ZYEONEYSNIUGRA-UHFFFAOYSA-O
P2H

wwPDB Information

Atom count

39 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-07-30

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



P2H : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C7 C C7 N N N 0 -0.924 0.127 -1.306
2 C8 C C8 N N N 0 -1.631 0.375 0.028
3 P9 P P9 N N N 0 -2.155 -1.217 0.744
4 O10 O O10 N N N 0 -0.863 -2.147 0.987
5 O11 O O11 N N N 0 -2.899 -0.956 2.147
6 N12 N N12 N Y N 1 0.323 -0.605 -1.068
7 O12 O O12 N N N 0 -3.083 -1.896 -0.188
8 C13 C C13 N Y N 0 0.336 -1.915 -1.22
9 O13 O O13 N N N 0 -0.735 1.031 0.928
10 C14 C C14 N Y N 0 1.491 -2.646 -1.006
11 P14 P P14 N N N 0 -3.094 1.428 -0.247
12 C15 C C15 N Y N 0 2.648 -1.988 -0.627
13 O15 O O15 N N N 0 -2.648 2.782 -0.995
14 C16 C C16 N Y N 0 2.602 -0.599 -0.475
15 O16 O O16 N N N 0 -4.16 0.638 -1.159
16 C17 C C17 N Y N 0 1.401 0.065 -0.714
17 O17 O O17 N N N 0 -3.712 1.764 1.055
18 C18 C C18 N Y N 0 3.814 0.156 -0.07
19 C19 C C19 N Y N 0 5.011 -0.517 0.162
20 C20 C C20 N Y N 0 6.135 0.19 0.539
21 C21 C C21 N Y N 0 6.074 1.564 0.686
22 C22 C C22 N Y N 0 4.888 2.237 0.456
23 C23 C C23 N Y N 0 3.759 1.541 0.074
24 H7 H H7 N N N 0 -1.571 -0.46 -1.957
25 H7A H H7A N N N 0 -0.699 1.082 -1.781
26 H13 H H13 N N N 0 -0.568 -2.425 -1.516
27 HO13 H HO13 N N N 0 0.067 0.527 1.12
28 H14 H H14 N N N 0 1.489 -3.718 -1.133
29 H15 H H15 N N N 0 3.564 -2.534 -0.452
30 H17 H H17 N N N 0 1.352 1.138 -0.604
31 H19 H H19 N N N 0 5.06 -1.59 0.049
32 H20 H H20 N N N 0 7.064 -0.33 0.719
33 H21 H H21 N N N 0 6.956 2.114 0.981
34 H22 H H22 N N N 0 4.845 3.31 0.572
35 H23 H H23 N N N 0 2.834 2.068 -0.11
36 H131 H H131 N N N 0 -1.067 -3.013 1.367
37 H141 H H141 N N N 0 -2.349 -0.514 2.808
38 H151 H H151 N N N 0 -2.167 2.635 -1.821
39 H16 H H16 N N N 0 -4.965 1.139 -1.346



P2H : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 C8 C C sing 1.53 N N
2 C7 N12 C N sing 1.47 N N
3 C7 H7 C H sing 1.09 N N
4 C7 H7A C H sing 1.09 N N
5 C8 P9 C P sing 1.82 N N
6 C8 O13 C O sing 1.43 N N
7 C8 P14 C P sing 1.82 N N
8 P9 O10 P O sing 1.61 N N
9 P9 O11 P O sing 1.61 N N
10 P9 O12 P O doub 1.48 N N
11 N12 C13 N C doub 1.32 N Y
12 N12 C17 N C sing 1.32 N Y
13 C13 C14 C C sing 1.38 N Y
14 C13 H13 C H sing 1.08 N N
15 O13 HO13 O H sing 0.97 N N
16 C14 C15 C C doub 1.38 N Y
17 C14 H14 C H sing 1.08 N N
18 P14 O15 P O sing 1.61 N N
19 P14 O16 P O sing 1.61 N N
20 P14 O17 P O doub 1.48 N N
21 C15 C16 C C sing 1.4 N Y
22 C15 H15 C H sing 1.08 N N
23 C16 C17 C C doub 1.39 N Y
24 C16 C18 C C sing 1.48 N Y
25 C17 H17 C H sing 1.08 N N
26 C18 C19 C C doub 1.39 N Y
27 C18 C23 C C sing 1.39 N Y
28 C19 C20 C C sing 1.38 N Y
29 C19 H19 C H sing 1.08 N N
30 C20 C21 C C doub 1.38 N Y
31 C20 H20 C H sing 1.08 N N
32 C21 C22 C C sing 1.38 N Y
33 C21 H21 C H sing 1.08 N N
34 C22 C23 C C doub 1.38 N Y
35 C22 H22 C H sing 1.08 N N
36 C23 H23 C H sing 1.08 N N
37 O10 H131 O H sing 0.97 N N
38 O11 H141 O H sing 0.97 N N
39 O15 H151 O H sing 0.97 N N
40 O16 H16 O H sing 0.97 N N



P2H : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
P2H 3icm Open in New Window Bound ligand 1 1
P2H 4jzb Open in New Window Bound ligand 2 1