Chemical Components in the PDB

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P25 : Summary

Code

P25

One-letter code

X

Molecule name

PENTYL TRIHYDROGEN DIPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 pentyl trihydrogen diphosphate
OpenEye OEToolkits 1.5.0 pentyl phosphono hydrogen phosphate

Formula

C5 H14 O7 P2

Formal charge

0

Molecular weight

248.108 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OP(=O)(OCCCCC)O)(O)O
SMILES CACTVS 3.341 CCCCCO[P](O)(=O)O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 CCCCCOP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 CCCCCO[P@](O)(=O)O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCO[P@@](=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C5H14O7P2/c1-2-3-4-5-11-14(9,10)12-13(6,7)8/h2-5H2,1H3,(H,9,10)(H2,6,7,8)

IUPAC InChI key

VFFCVKZHJFIUBM-UHFFFAOYSA-N
P25

wwPDB Information

Atom count

28 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-07-01

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



P25 : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C4 N N N 0 5.735 0.272 0.445
2 CM4 C CM4 N N N 0 6.896 0.125 -0.539
3 C5 C C5 N N N 0 4.413 0.022 -0.284
4 C6 C C6 N N N 0 3.251 0.169 0.701
5 C7 C C7 N N N 0 1.93 -0.082 -0.029
6 O7 O O7 N N N 0 0.845 0.056 0.891
7 PA P PA R N N 0 -0.507 -0.219 0.061
8 O1A O O1A N N N 0 -0.561 0.688 -1.108
9 O2A O O2A N N N 0 -0.524 -1.748 -0.446
10 O3A O O3A N N N 0 -1.782 0.047 1.007
11 PB P PB N N N 0 -3.065 0.149 0.04
12 O1B O O1B N N N 0 -3.021 -0.944 -0.956
13 O2B O O2B N N N 0 -4.409 0.021 0.918
14 O3B O O3B N N N 0 -3.054 1.569 -0.72
15 H41 H 1H4 N N N 0 5.848 -0.453 1.251
16 H42 H 2H4 N N N 0 5.735 1.28 0.861
17 HM41 H 1HM4 N N N 0 7.838 0.303 -0.02
18 HM42 H 2HM4 N N N 0 6.896 -0.883 -0.955
19 HM43 H 3HM4 N N N 0 6.783 0.85 -1.345
20 H51 H 1H5 N N N 0 4.3 0.747 -1.09
21 H52 H 2H5 N N N 0 4.412 -0.986 -0.699
22 H61 H 1H6 N N N 0 3.364 -0.557 1.507
23 H62 H 2H6 N N N 0 3.252 1.176 1.116
24 H71 H 1H7 N N N 0 1.817 0.644 -0.835
25 H72 H 2H7 N N N 0 1.929 -1.089 -0.444
26 H2A H H2A N N N 0 -0.488 -2.304 0.344
27 H2B H H2B N N N 0 -5.152 0.087 0.302
28 H3B H H3B N N N 0 -3.084 2.252 -0.036



P25 : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 CM4 C C sing 1.53 N N
2 C4 C5 C C sing 1.53 N N
3 C4 H41 C H sing 1.09 N N
4 C4 H42 C H sing 1.09 N N
5 CM4 HM41 C H sing 1.09 N N
6 CM4 HM42 C H sing 1.09 N N
7 CM4 HM43 C H sing 1.09 N N
8 C5 C6 C C sing 1.53 N N
9 C5 H51 C H sing 1.09 N N
10 C5 H52 C H sing 1.09 N N
11 C6 C7 C C sing 1.53 N N
12 C6 H61 C H sing 1.09 N N
13 C6 H62 C H sing 1.09 N N
14 C7 O7 C O sing 1.43 N N
15 C7 H71 C H sing 1.09 N N
16 C7 H72 C H sing 1.09 N N
17 O7 PA O P sing 1.61 N N
18 PA O1A P O doub 1.48 N N
19 PA O2A P O sing 1.61 N N
20 PA O3A P O sing 1.61 N N
21 O2A H2A O H sing 0.97 N N
22 O3A PB O P sing 1.61 N N
23 PB O1B P O doub 1.48 N N
24 PB O2B P O sing 1.61 N N
25 PB O3B P O sing 1.61 N N
26 O2B H2B O H sing 0.97 N N
27 O3B H3B O H sing 0.97 N N



P25 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
P25 1t9b Open in New Window Bound ligand 1 1
P25 1t9d Open in New Window Bound ligand 2 1