Chemical Components in the PDB

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  • A6P (Stereoisomer)
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RTG : Summary

Code

RTG

One-letter code

X

Molecule name

6-O-phosphono-alpha-L-idopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 6-O-phosphono-alpha-L-idopyranose
OpenEye OEToolkits 2.0.7 [(2~{S},3~{S},4~{S},5~{R},6~{R})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate

Formula

C6 H13 O9 P

Formal charge

0

Molecular weight

260.136 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(OCC1OC(C(C(C1O)O)O)O)O
SMILES CACTVS 3.385 O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.7 C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O
Canonical SMILES CACTVS 3.385 O[C@@H]1O[C@@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.7 C([C@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3+,4-,5+,6+/m0/s1

IUPAC InChI key

NBSCHQHZLSJFNQ-DSOBHZJASA-N
RTG

wwPDB Information

Atom count

29 (16 without Hydrogen)

Polymer type

Saccharide

Type description

L-saccharide, alpha linking

Type code

ATOMS

Is modified

Yes

Standard parent

Z0F

Defined at

2020-02-25

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



RTG : Atoms of Molecule

Total Number of Atoms: 29
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAH O OAH N N N 0 -3.523 -0.97 -1.122
2 PBA P PBA N N N 0 -3.32 0.041 -0.06
3 OAI O OAI N N N 0 -4.102 1.393 -0.449
4 OAJ O OAJ N N N 0 -3.888 -0.525 1.336
5 O6 O O6 N N N 0 -1.747 0.354 0.089
6 C6 C C6 N N N 0 -0.771 -0.661 0.327
7 C5 C C5 S N N 0 0.617 -0.023 0.415
8 O5 O O5 N N N 0 0.962 0.544 -0.851
9 C4 C C4 S N N 0 1.647 -1.092 0.791
10 O4 O O4 N N N 0 1.619 -2.144 -0.176
11 C3 C C3 S N N 0 3.042 -0.458 0.818
12 O3 O O3 N N N 0 3.089 0.55 1.829
13 C2 C C2 R N N 0 3.331 0.172 -0.548
14 O2 O O2 N N N 0 3.347 -0.846 -1.55
15 C1 C C1 R N N 0 2.236 1.192 -0.872
16 O1 O O1 N N N 0 2.255 2.238 0.101
17 H6 H H6 N N N 0 -5.056 1.279 -0.555
18 H7 H H7 N N N 0 -3.788 0.086 2.079
19 H61 H H61 N N N 0 -0.996 -1.171 1.264
20 H62 H H62 N N N 0 -0.788 -1.381 -0.492
21 H5 H H5 N N N 0 0.61 0.759 1.174
22 H4 H H4 N N N 0 1.411 -1.495 1.775
23 HO4 H HO4 N N N 0 2.249 -2.856 0.0
24 H3 H H3 N N N 0 3.787 -1.225 1.03
25 HO3 H HO3 N N N 0 3.945 0.994 1.903
26 H2 H H2 N N N 0 4.298 0.674 -0.52
27 HO2 H HO2 N N N 0 3.525 -0.517 -2.442
28 H1 H H1 N N N 0 2.412 1.613 -1.862
29 HO1 H HO1 N N Y 0 1.585 2.921 -0.042



RTG : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAH PBA O P doub 1.48 N N
2 PBA OAI P O sing 1.61 N N
3 PBA O6 P O sing 1.61 N N
4 PBA OAJ P O sing 1.61 N N
5 O6 C6 O C sing 1.43 N N
6 C6 C5 C C sing 1.53 N N
7 C5 O5 C O sing 1.43 N N
8 C5 C4 C C sing 1.53 N N
9 O5 C1 O C sing 1.43 N N
10 C4 O4 C O sing 1.43 N N
11 C4 C3 C C sing 1.53 N N
12 C3 C2 C C sing 1.53 N N
13 C3 O3 C O sing 1.43 N N
14 C2 C1 C C sing 1.53 N N
15 C2 O2 C O sing 1.43 N N
16 C1 O1 C O sing 1.43 N N
17 OAI H6 O H sing 0.97 N N
18 OAJ H7 O H sing 0.97 N N
19 C6 H61 C H sing 1.09 N N
20 C6 H62 C H sing 1.09 N N
21 C5 H5 C H sing 1.09 N N
22 C4 H4 C H sing 1.09 N N
23 O4 HO4 O H sing 0.97 N N
24 C3 H3 C H sing 1.09 N N
25 O3 HO3 O H sing 0.97 N N
26 C2 H2 C H sing 1.09 N N
27 O2 HO2 O H sing 0.97 N N
28 C1 H1 C H sing 1.09 N N
29 O1 HO1 O H sing 0.97 N N



RTG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RTG 4ipn Open in New Window s 2 1