Chemical Components in the PDB

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RB3 : Summary

Code

RB3

One-letter code

X

Molecule name

(1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL (3R)-3-HYDROXYBUTANOATE

Synonyms

METHYL (3R)-3-{[(3R)-3-{[(3R)-3-HYDROXYBUTANOYL]OXY}BUTANOYL]OXY}BUTANOATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R)-3-{[(1R)-3-methoxy-1-methyl-3-oxopropyl]oxy}-1-methyl-3-oxopropyl (3R)-3-hydroxybutanoate
OpenEye OEToolkits 1.5.0 methyl (3R)-3-[(3R)-3-[(3R)-3-hydroxybutanoyl]oxybutanoyl]oxybutanoate

Formula

C13 H22 O7

Formal charge

0

Molecular weight

290.31 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OC(C)CC(=O)OC(CC(=O)OC)C)CC(O)C
SMILES CACTVS 3.341 COC(=O)C[CH](C)OC(=O)C[CH](C)OC(=O)C[CH](C)O
SMILES OpenEye OEToolkits 1.5.0 CC(CC(=O)OC(C)CC(=O)OC(C)CC(=O)OC)O
Canonical SMILES CACTVS 3.341 COC(=O)C[C@@H](C)OC(=O)C[C@@H](C)OC(=O)C[C@@H](C)O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@H](CC(=O)O[C@H](C)CC(=O)O[C@H](C)CC(=O)OC)O

IUPAC InChI

InChI=1S/C13H22O7/c1-8(14)5-12(16)19-10(3)7-13(17)20-9(2)6-11(15)18-4/h8-10,14H,5-7H2,1-4H3/t8-,9-,10-/m1/s1

IUPAC InChI key

WGAHBMKAEWUQKL-OPRDCNLKSA-N
RB3

wwPDB Information

Atom count

42 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-12-27

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



RB3 : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1M O O1M N N N 0 -1.015 1.593 -6.64
2 C1A C C1A N N N 0 -1.394 1.891 -5.361
3 O1A O O1A N N N 0 -1.789 2.98 -4.967
4 C2A C C2A N N N 0 -1.249 0.649 -4.507
5 C3A C C3A R N N 0 -0.961 0.98 -3.042
6 C4A C C4A N N N 0 0.304 1.818 -2.906
7 O3A O O3A N N N 0 -2.058 1.725 -2.519
8 C2B C C2B N N N 0 -4.365 2.132 -2.688
9 C1B C C1B N N N 0 -3.272 1.093 -2.547
10 O1B O O1B N N N 0 -3.449 -0.115 -2.469
11 C3B C C3B R N N 0 -5.601 1.584 -3.404
12 C4B C C4B N N N 0 -6.66 2.666 -3.577
13 O3B O O3B N N N 0 -5.211 1.12 -4.694
14 C1C C C1C N N N 0 -6.214 0.598 -5.466
15 O1C O O1C N N N 0 -7.389 0.504 -5.139
16 C2C C C2C N N N 0 -5.636 0.158 -6.795
17 C3C C C3C R N N 0 -4.963 1.307 -7.547
18 C4C C C4C N N N 0 -4.439 0.844 -8.901
19 O3C O O3C N N N 0 -5.926 2.337 -7.76
20 C1 C C1 N N N 0 -1.1 2.673 -7.576
21 H2A1 H 1H2A N N N 0 -0.429 0.053 -4.925
22 H2A2 H 2H2A N N N 0 -2.187 0.088 -4.584
23 H3A H H3A N N N 0 -0.861 0.063 -2.45
24 H4A1 H 1H4A N N N 0 0.205 2.767 -3.445
25 H4A2 H 2H4A N N N 0 1.178 1.284 -3.291
26 H4A3 H 3H4A N N N 0 0.486 2.07 -1.856
27 H2B1 H 1H2B N N N 0 -3.95 2.976 -3.25
28 H2B2 H 2H2B N N N 0 -4.636 2.46 -1.678
29 H3B H H3B N N N 0 -6.025 0.738 -2.852
30 H4B1 H 1H4B N N N 0 -6.275 3.499 -4.174
31 H4B2 H 2H4B N N N 0 -6.996 3.052 -2.61
32 H4B3 H 3H4B N N N 0 -7.528 2.269 -4.113
33 H2C1 H 1H2C N N N 0 -6.457 -0.253 -7.394
34 H2C2 H 2H2C N N N 0 -4.903 -0.63 -6.587
35 H1 H H1 N N N 0 -4.141 1.728 -6.958
36 H4C1 H 1H4C N N N 0 -5.254 0.471 -9.53
37 H4C2 H 2H4C N N N 0 -3.69 0.054 -8.789
38 H4C3 H 3H4C N N N 0 -3.982 1.681 -9.441
39 H3C H H3C N N N 0 -5.976 2.473 -8.719
40 H11 H 1H1 N N N 0 -0.696 2.353 -8.539
41 H12 H 2H1 N N N 0 -0.534 3.529 -7.198
42 H13 H 3H1 N N N 0 -2.148 2.956 -7.698



RB3 : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1M C1A O C sing 1.37 N N
2 O1M C1 O C sing 1.43 N N
3 C1A O1A C O doub 1.22 N N
4 C1A C2A C C sing 1.51 N N
5 C2A C3A C C sing 1.53 N N
6 C2A H2A1 C H sing 1.1 N N
7 C2A H2A2 C H sing 1.1 N N
8 C3A C4A C C sing 1.52 N N
9 C3A O3A C O sing 1.43 N N
10 C3A H3A C H sing 1.1 N N
11 C4A H4A1 C H sing 1.1 N N
12 C4A H4A2 C H sing 1.09 N N
13 C4A H4A3 C H sing 1.1 N N
14 O3A C1B O C sing 1.37 N N
15 C1B O1B C O doub 1.22 N N
16 C1B C2B C C sing 1.51 N N
17 C2B C3B C C sing 1.53 N N
18 C2B H2B1 C H sing 1.1 N N
19 C2B H2B2 C H sing 1.1 N N
20 C3B C4B C C sing 1.52 N N
21 C3B O3B C O sing 1.43 N N
22 C3B H3B C H sing 1.1 N N
23 C4B H4B1 C H sing 1.09 N N
24 C4B H4B2 C H sing 1.09 N N
25 C4B H4B3 C H sing 1.09 N N
26 O3B C1C O C sing 1.37 N N
27 C1C O1C C O doub 1.22 N N
28 C1C C2C C C sing 1.51 N N
29 C2C C3C C C sing 1.53 N N
30 C2C H2C1 C H sing 1.1 N N
31 C2C H2C2 C H sing 1.1 N N
32 C3C C4C C C sing 1.52 N N
33 C3C O3C C O sing 1.43 N N
34 C3C H1 C H sing 1.1 N N
35 C4C H4C1 C H sing 1.09 N N
36 C4C H4C2 C H sing 1.09 N N
37 C4C H4C3 C H sing 1.1 N N
38 O3C H3C O H sing 0.97 N N
39 C1 H11 C H sing 1.09 N N
40 C1 H12 C H sing 1.09 N N
41 C1 H13 C H sing 1.09 N N



RB3 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
RB3 2d81 Open in New Window Bound ligand 1 1
RB3 4btv Open in New Window Bound ligand 2 1