Chemical Components in the PDB

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P6F : Summary

Code

P6F

One-letter code

X

Molecule name

1,6-di-O-phosphono-D-fructose

Systematic names

ProgramVersionName
ACDLabs 10.04 1,6-di-O-phosphono-D-fructose
OpenEye OEToolkits 1.5.0 [(3S,4R,5R)-3,4,5-trihydroxy-2-oxo-6-phosphonooxy-hexyl] dihydrogen phosphate

Formula

C6 H14 O12 P2

Formal charge

0

Molecular weight

340.116 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC(=O)C(O)C(O)C(O)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)C(=O)CO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 C(C(C(C(C(=O)COP(=O)(O)O)O)O)O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)C(=O)CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@H]([C@H]([C@@H](C(=O)COP(=O)(O)O)O)O)O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C6H14O12P2/c7-3(1-17-19(11,12)13)5(9)6(10)4(8)2-18-20(14,15)16/h3,5-7,9-10H,1-2H2,(H2,11,12,13)(H2,14,15,16)/t3-,5-,6-/m1/s1

IUPAC InChI key

XPYBSIWDXQFNMH-UYFOZJQFSA-N
P6F

wwPDB Information

Atom count

34 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-03-02

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



P6F : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P1 P P1 N N N 0 5.226 0.938 -0.014
2 O1P O O1P N N N 0 5.787 0.742 -1.51
3 O2P O O2P N N N 0 6.428 0.751 1.04
4 O3P O O3P N N N 0 4.656 2.297 0.124
5 O1 O O1 N N N 0 4.081 -0.155 0.278
6 C1 C C1 N N N 0 2.835 -0.184 -0.421
7 C2 C C2 N N N 0 1.997 -1.327 0.092
8 O2 O O2 N N N 0 2.423 -2.043 0.965
9 C3 C C3 S N N 0 0.627 -1.575 -0.486
10 O3 O O3 N N N 0 0.182 -2.88 -0.11
11 C4 C C4 R N N 0 -0.35 -0.528 0.051
12 O4 O O4 N N N 0 -0.324 -0.539 1.48
13 C5 C C5 R N N 0 -1.764 -0.853 -0.435
14 O5 O O5 N N N 0 -1.791 -0.842 -1.864
15 C6 C C6 N N N 0 -2.742 0.194 0.101
16 O6 O O6 N N N 0 -4.076 -0.173 -0.255
17 P2 P P2 N N N 0 -5.364 0.705 0.148
18 O4P O O4P N N N 0 -5.381 0.912 1.613
19 O5P O O5P N N N 0 -5.295 2.132 -0.595
20 O6P O O6P N N N 0 -6.703 -0.069 -0.3
21 HO1P H HO1P N N N 0 6.176 -0.128 -1.673
22 HO2P H HO2P N N N 0 7.155 1.378 0.923
23 H1 H H1 N N N 0 2.306 0.756 -0.259
24 H1A H H1A N N N 0 3.019 -0.317 -1.487
25 H3 H H3 N N N 0 0.673 -1.506 -1.572
26 HO3 H HO3 N N N 0 0.117 -3.013 0.846
27 H4 H H4 N N N 0 -0.06 0.459 -0.31
28 HO4 H HO4 N N N 0 -0.572 -1.388 1.871
29 H5 H H5 N N N 0 -2.054 -1.84 -0.075
30 HO5 H HO5 N N N 0 -1.542 0.007 -2.255
31 HO6P H HO6P N N N 0 -7.52 0.403 -0.088
32 H6 H H6 N N N 0 -2.657 0.248 1.187
33 H6A H H6A N N N 0 -2.505 1.167 -0.33
34 HO5P H HO5P N N N 0 -5.281 2.072 -1.56



P6F : Chemical Bonds

Total Number of Bonds: 33
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3P P1 O P doub 1.48 N N
2 O1P P1 O P sing 1.61 N N
3 P1 O1 P O sing 1.61 N N
4 P1 O2P P O sing 1.61 N N
5 O1P HO1P O H sing 0.97 N N
6 O2P HO2P O H sing 0.97 N N
7 C1 O1 C O sing 1.43 N N
8 C1 C2 C C sing 1.51 N N
9 C1 H1 C H sing 1.09 N N
10 C1 H1A C H sing 1.09 N N
11 C3 C2 C C sing 1.51 N N
12 C2 O2 C O doub 1.21 N N
13 C4 C3 C C sing 1.53 N N
14 C3 O3 C O sing 1.43 N N
15 C3 H3 C H sing 1.09 N N
16 O3 HO3 O H sing 0.97 N N
17 C5 C4 C C sing 1.53 N N
18 C4 O4 C O sing 1.43 N N
19 C4 H4 C H sing 1.09 N N
20 O4 HO4 O H sing 0.97 N N
21 O5 C5 O C sing 1.43 N N
22 C6 C5 C C sing 1.53 N N
23 C5 H5 C H sing 1.09 N N
24 O5 HO5 O H sing 0.97 N N
25 O6 C6 O C sing 1.43 N N
26 C6 H6 C H sing 1.09 N N
27 C6 H6A C H sing 1.09 N N
28 P2 O6 P O sing 1.61 N N
29 O4P P2 O P doub 1.48 N N
30 O6P P2 O P sing 1.61 N N
31 P2 O5P P O sing 1.61 N N
32 O5P HO5P O H sing 0.97 N N
33 O6P HO6P O H sing 0.97 N N



P6F : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
P6F 3gb6 Open in New Window Bound ligand 2 1
P6F 3t2d Open in New Window Bound ligand 1 1
P6F 5f2g Open in New Window Bound ligand 1 1
P6F 5f4s Open in New Window Bound ligand 1 1
P6F 5tkl Open in New Window Bound ligand 1 1
P6F 5tkn Open in New Window Bound ligand 1 1
P6F 5tkp Open in New Window Bound ligand 1 1
P6F 5ucp Open in New Window Bound ligand 1 1
P6F 5ud3 Open in New Window Bound ligand 2 1