Chemical Components in the PDB

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S3P : Summary

Code

S3P

One-letter code

X

Molecule name

SHIKIMATE-3-PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,4S,5R)-4,5-dihydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid
OpenEye OEToolkits 1.5.0 (3R,4S,5R)-4,5-dihydroxy-3-phosphonooxy-cyclohexene-1-carboxylic acid

Formula

C7 H11 O8 P

Formal charge

0

Molecular weight

254.131 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C1=CC(OP(=O)(O)O)C(O)C(O)C1
SMILES CACTVS 3.341 O[CH]1CC(=C[CH](O[P](O)(O)=O)[CH]1O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C=C1C(=O)O)OP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1CC(=C[C@@H](O[P](O)(O)=O)[C@H]1O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)OP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C7H11O8P/c8-4-1-3(7(10)11)2-5(6(4)9)15-16(12,13)14/h2,4-6,8-9H,1H2,(H,10,11)(H2,12,13,14)/t4-,5-,6+/m1/s1

IUPAC InChI key

QYOJSKGCWNAKGW-PBXRRBTRSA-N
S3P

wwPDB Information

Atom count

27 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2000-11-16

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



S3P : Atoms of Molecule

Total Number of Atoms: 27
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -0.284 0.031 2.05
2 C2 C C2 N N N 0 -0.683 -0.029 0.797
3 C3 C C3 R N N 0 0.251 -0.029 -0.376
4 C4 C C4 S N N 0 1.638 0.47 0.048
5 C5 C C5 R N N 0 2.062 -0.299 1.304
6 C6 C C6 N N N 0 1.156 0.117 2.464
7 C7 C C7 N N N 0 -1.307 0.014 3.104
8 O1 O O1 N N N 0 -0.266 0.829 -1.394
9 O2 O O2 N N N 0 1.577 1.868 0.335
10 O3 O O3 N N N 0 1.933 -1.703 1.074
11 O4 O O4 N N N 0 -0.941 0.074 4.4
12 O5 O O5 N N N 0 -2.484 -0.053 2.808
13 P1 P P1 N N N 0 -0.494 -0.082 -2.701
14 O6 O O6 N N N 0 -1.454 -1.163 -2.388
15 O7 O O7 N N N 0 -1.08 0.826 -3.894
16 O8 O O8 N N N 0 0.909 -0.726 -3.157
17 H2 H H2 N N N 0 -1.744 -0.082 0.603
18 H3 H H3 N N N 0 0.338 -1.042 -0.769
19 H4 H H4 N N N 0 2.353 0.291 -0.754
20 H5 H H5 N N N 0 3.098 -0.062 1.546
21 H61 H 1H6 N N N 0 1.327 -0.544 3.313
22 H62 H 2H6 N N N 0 1.388 1.142 2.754
23 HO2 H HO2 N N N 0 2.468 2.138 0.597
24 HO3 H HO3 N N N 0 2.203 -2.147 1.89
25 HO4 H HO4 N N N 0 -1.615 0.063 5.094
26 HO7 H HO7 N N N 0 -1.201 0.243 -4.656
27 HO8 H HO8 N N N 0 1.504 0.009 -3.352



S3P : 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 C1 C2 C C doub 1.32 N N
2 C1 C6 C C sing 1.5 N N
3 C1 C7 C C sing 1.47 N N
4 C2 C3 C C sing 1.5 N N
5 C2 H2 C H sing 1.08 N N
6 C3 C4 C C sing 1.53 N N
7 C3 O1 C O sing 1.43 N N
8 C3 H3 C H sing 1.09 N N
9 C4 C5 C C sing 1.53 N N
10 C4 O2 C O sing 1.43 N N
11 C4 H4 C H sing 1.09 N N
12 C5 C6 C C sing 1.53 N N
13 C5 O3 C O sing 1.43 N N
14 C5 H5 C H sing 1.09 N N
15 C6 H61 C H sing 1.09 N N
16 C6 H62 C H sing 1.09 N N
17 C7 O4 C O sing 1.35 N N
18 C7 O5 C O doub 1.22 N N
19 O1 P1 O P sing 1.61 N N
20 O2 HO2 O H sing 0.97 N N
21 O3 HO3 O H sing 0.97 N N
22 O4 HO4 O H sing 0.97 N N
23 P1 O6 P O doub 1.48 N N
24 P1 O7 P O sing 1.61 N N
25 P1 O8 P O sing 1.61 N N
26 O7 HO7 O H sing 0.97 N N
27 O8 HO8 O H sing 0.97 N N



S3P : Used in PDB Entries

Total Number of PDB Entries: 32
Ligand Code PDB Entry ID Type Total Distinct
S3P 1g6s Open in New Window Bound ligand 1 1
S3P 1g6t Open in New Window Bound ligand 1 1
S3P 1mi4 Open in New Window Bound ligand 1 1
S3P 1rf6 Open in New Window Bound ligand 4 1
S3P 2gg6 Open in New Window Bound ligand 1 1
S3P 2gga Open in New Window Bound ligand 1 1
S3P 2ggd Open in New Window Bound ligand 1 1
S3P 2iyy Open in New Window Bound ligand 1 1
S3P 2iyz Open in New Window Bound ligand 1 1
S3P 2o0b Open in New Window Bound ligand 1 1
S3P 2o0d Open in New Window Bound ligand 1 1
S3P 2o0e Open in New Window Bound ligand 1 1
S3P 2qfq Open in New Window Bound ligand 1 1
S3P 2qfs Open in New Window Bound ligand 1 1
S3P 2qft Open in New Window Bound ligand 1 1
S3P 2qfu Open in New Window Bound ligand 1 1
S3P 3fjx Open in New Window Bound ligand 1 1
S3P 3fjz Open in New Window Bound ligand 1 1
S3P 3fk0 Open in New Window Bound ligand 1 1
S3P 3fk1 Open in New Window Bound ligand 1 1
S3P 3muf Open in New Window Bound ligand 1 1
S3P 3nvs Open in New Window Bound ligand 1 1
S3P 3slh Open in New Window Bound ligand 4 1
S3P 4znd Open in New Window Bound ligand 1 1
S3P 7tbu Open in New Window Bound ligand 2 1
S3P 7tm5 Open in New Window Bound ligand 2 1
S3P 7tm6 Open in New Window Bound ligand 2 1
S3P 8umj Open in New Window Bound ligand 2 1
S3P 8umk Open in New Window Bound ligand 2 1
S3P 8uml Open in New Window Bound ligand 2 1
S3P 8umm Open in New Window Bound ligand 2 1
S3P 8umn Open in New Window Bound ligand 2 1