Chemical Components in the PDB

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CDI : Summary

Code

CDI

One-letter code

X

Molecule name

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,4S,6S,7R)-6-(hydroxymethyl)-6-methyl-1,3,5,2,4-trioxadiphosphocane-2,4,7-triol 2,4-dioxide
OpenEye OEToolkits 1.5.0 (2R,4S,6S,7R)-2,4-dihydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5-trioxa-2$l^{5},4$l^{5}-diphosphacyclooctan-7-ol

Formula

C5 H12 O9 P2

Formal charge

0

Molecular weight

278.091 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P1(OP(=O)(OCC(O)C(O1)(C)CO)O)O
SMILES CACTVS 3.341 C[C]1(CO)O[P](O)(=O)O[P](O)(=O)OC[CH]1O
SMILES OpenEye OEToolkits 1.5.0 CC1(C(COP(=O)(OP(=O)(O1)O)O)O)CO
Canonical SMILES CACTVS 3.341 C[C@@]1(CO)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@]1([C@@H](CO[P@](=O)(O[P@](=O)(O1)O)O)O)CO

IUPAC InChI

InChI=1S/C5H12O9P2/c1-5(3-6)4(7)2-12-15(8,9)14-16(10,11)13-5/h4,6-7H,2-3H2,1H3,(H,8,9)(H,10,11)/t4-,5+/m1/s1

IUPAC InChI key

SFRQRNJMIIUYDI-UHNVWZDZSA-N
CDI

wwPDB Information

Atom count

28 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-09-18

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CDI : 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 -0.474 -0.373 -3.149
2 C3 C C3 S N N 0 -0.176 0.115 -1.708
3 OB4 O OB4 N N N 0 1.06 -0.511 -1.316
4 PB P PB S N N 0 1.4 -0.203 0.22
5 OB2 O OB2 N N N 0 2.917 -0.697 0.505
6 OB3 O OB3 N N N 0 1.303 1.22 0.555
7 PA P PA R N N 0 -0.445 -0.024 2.011
8 OA3 O OA3 N N N 0 -0.891 1.179 1.041
9 OA1 O OA1 N N N 0 -1.745 -0.749 2.624
10 OA2 O OA2 N N N 0 0.385 0.509 3.117
11 C1 C C1 N N N 0 -1.855 0.694 0.127
12 C2 C C2 R N N 0 -1.318 -0.374 -0.818
13 O1 O O1 N N N 0 -2.397 -0.818 -1.664
14 C5 C C5 N N N 0 -0.062 1.63 -1.762
15 O2 O O2 N N N 0 0.592 0.019 -4.015
16 OB1 O OB1 N N N 0 0.415 -1.085 1.158
17 HC41 H 1HC4 N N N 0 -0.564 -1.459 -3.153
18 HC42 H 2HC4 N N N 0 -1.407 0.069 -3.497
19 HB2O H OHB2 N N N 0 3.103 -0.504 1.434
20 HA1O H OHA1 N N N 0 -1.426 -1.464 3.191
21 HC11 H 1HC1 N N N 0 -2.687 0.258 0.703
22 HC12 H 2HC1 N N N 0 -2.285 1.523 -0.438
23 HC2 H HC2 N N N 0 -0.989 -1.247 -0.244
24 HO1 H HO1 N N N 0 -3.08 -1.177 -1.081
25 HC51 H 1HC5 N N N 0 0.747 1.909 -2.437
26 HC52 H 2HC5 N N N 0 -0.999 2.052 -2.125
27 HC53 H 3HC5 N N N 0 0.147 2.015 -0.764
28 HO2 H HO2 N N N 0 0.367 -0.303 -4.898



CDI : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 C3 C C sing 1.55 N N
2 C4 O2 C O sing 1.43 N N
3 C4 HC41 C H sing 1.09 N N
4 C4 HC42 C H sing 1.09 N N
5 C3 OB4 C O sing 1.44 N N
6 C3 C2 C C sing 1.53 N N
7 C3 C5 C C sing 1.52 N N
8 OB4 PB O P sing 1.6 N N
9 PB OB2 P O sing 1.62 N N
10 PB OB3 P O doub 1.47 N N
11 PB OB1 P O sing 1.62 N N
12 OB2 HB2O O H sing 0.97 N N
13 PA OA3 P O sing 1.61 N N
14 PA OA1 P O sing 1.61 N N
15 PA OA2 P O doub 1.48 N N
16 PA OB1 P O sing 1.61 N N
17 OA3 C1 O C sing 1.41 N N
18 OA1 HA1O O H sing 0.97 N N
19 C1 C2 C C sing 1.52 N N
20 C1 HC11 C H sing 1.1 N N
21 C1 HC12 C H sing 1.09 N N
22 C2 O1 C O sing 1.44 N N
23 C2 HC2 C H sing 1.1 N N
24 O1 HO1 O H sing 0.97 N N
25 C5 HC51 C H sing 1.09 N N
26 C5 HC52 C H sing 1.09 N N
27 C5 HC53 C H sing 1.09 N N
28 O2 HO2 O H sing 0.97 N N



CDI : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
CDI 1h48 Open in New Window Bound ligand 6 1
CDI 1jy8 Open in New Window Bound ligand 1 1
CDI 1knj Open in New Window Bound ligand 1 1
CDI 4g9p Open in New Window Bound ligand 1 1
CDI 4s38 Open in New Window Bound ligand 1 1