Chemical Components in the PDB

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28E : Summary

Code

28E

One-letter code

X

Molecule name

(2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol

Synonyms

Epicatechin

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
OpenEye OEToolkits 1.7.6 (2R,3R)-2-[3,4-bis(oxidanyl)phenyl]-3,4-dihydro-2H-chromene-3,5,7-triol

Formula

C15 H14 O6

Formal charge

0

Molecular weight

290.268 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Oc1ccc(cc1O)C3Oc2cc(O)cc(O)c2CC3O
SMILES CACTVS 3.385 O[CH]1Cc2c(O)cc(O)cc2O[CH]1c3ccc(O)c(O)c3
SMILES OpenEye OEToolkits 1.7.6 c1cc(c(cc1C2C(Cc3c(cc(cc3O2)O)O)O)O)O
Canonical SMILES CACTVS 3.385 O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c3ccc(O)c(O)c3
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(c(cc1[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)O)O)O)O

IUPAC InChI

InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15-/m1/s1

IUPAC InChI key

PFTAWBLQPZVEMU-UKRRQHHQSA-N
28E

wwPDB Information

Atom count

35 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-09-09

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



28E : Atoms of Molecule

Total Number of Atoms: 35
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAB O OAB N N N 0 4.852 -2.544 0.339
2 CAT C CAT N Y N 0 4.033 -1.463 0.255
3 CAK C CAK N Y N 0 4.572 -0.19 0.145
4 CAY C CAY N Y N 0 3.733 0.91 0.061
5 OAG O OAG N N N 0 4.262 2.157 -0.046
6 CBD C CBD N Y N 0 2.353 0.742 0.087
7 CAP C CAP N N N 0 1.474 1.964 0.004
8 CAN C CAN N Y N 0 2.658 -1.631 0.273
9 CBC C CBC N Y N 0 1.815 -0.528 0.192
10 OAR O OAR N N N 0 0.473 -0.737 0.209
11 CBF C CBF R N N 0 -0.373 0.377 0.498
12 CBE C CBE R N N 0 0.054 1.551 -0.392
13 OAQ O OAQ N N N 0 0.034 1.148 -1.763
14 CBA C CBA N Y N 0 -1.806 0.015 0.208
15 CAO C CAO N Y N 0 -2.821 0.527 0.996
16 CAV C CAV N Y N 0 -4.139 0.196 0.73
17 OAD O OAD N N N 0 -5.138 0.7 1.504
18 CAU C CAU N Y N 0 -4.44 -0.654 -0.33
19 OAC O OAC N N N 0 -5.733 -0.982 -0.595
20 CAI C CAI N Y N 0 -3.419 -1.164 -1.116
21 CAJ C CAJ N Y N 0 -2.105 -0.825 -0.849
22 H1 H H1 N N N 0 5.086 -2.927 -0.518
23 H2 H H2 N N N 0 5.643 -0.055 0.125
24 H3 H H3 N N N 0 4.407 2.445 -0.958
25 H4 H H4 N N N 0 1.45 2.46 0.974
26 H5 H H5 N N N 0 1.874 2.649 -0.744
27 H6 H H6 N N N 0 2.239 -2.623 0.353
28 H7 H H7 N N N 0 -0.269 0.654 1.547
29 H8 H H8 N N N 0 -0.627 2.39 -0.245
30 H9 H H9 N N N 0 0.31 1.84 -2.38
31 H10 H H10 N N N 0 -2.585 1.186 1.819
32 H11 H H11 N N N 0 -5.493 1.542 1.189
33 H12 H H12 N N N 0 -6.173 -0.38 -1.211
34 H13 H H13 N N N 0 -3.65 -1.824 -1.939
35 H14 H H14 N N N 0 -1.311 -1.22 -1.464



28E : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAG CAY O C sing 1.36 N N
2 CAY CAK C C doub 1.39 N Y
3 CAY CBD C C sing 1.39 N Y
4 CAK CAT C C sing 1.39 N Y
5 CAP CBD C C sing 1.51 N N
6 CAP CBE C C sing 1.53 N N
7 CBD CBC C C doub 1.38 N Y
8 CAT OAB C O sing 1.36 N N
9 CAT CAN C C doub 1.39 N Y
10 OAQ CBE O C sing 1.43 N N
11 CBE CBF C C sing 1.53 N N
12 CBC CAN C C sing 1.39 N Y
13 CBC OAR C O sing 1.36 N N
14 CBF OAR C O sing 1.43 N N
15 CBF CBA C C sing 1.51 N N
16 CBA CAJ C C doub 1.38 N Y
17 CBA CAO C C sing 1.38 N Y
18 CAJ CAI C C sing 1.38 N Y
19 CAO CAV C C doub 1.38 N Y
20 CAI CAU C C doub 1.39 N Y
21 CAV CAU C C sing 1.39 N Y
22 CAV OAD C O sing 1.36 N N
23 CAU OAC C O sing 1.36 N N
24 OAB H1 O H sing 0.97 N N
25 CAK H2 C H sing 1.08 N N
26 OAG H3 O H sing 0.97 N N
27 CAP H4 C H sing 1.09 N N
28 CAP H5 C H sing 1.09 N N
29 CAN H6 C H sing 1.08 N N
30 CBF H7 C H sing 1.09 N N
31 CBE H8 C H sing 1.09 N N
32 OAQ H9 O H sing 0.97 N N
33 CAO H10 C H sing 1.08 N N
34 OAD H11 O H sing 0.97 N N
35 OAC H12 O H sing 0.97 N N
36 CAI H13 C H sing 1.08 N N
37 CAJ H14 C H sing 1.08 N N



28E : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
28E 4ma6 Open in New Window Bound ligand 1 1
28E 6awt Open in New Window Bound ligand 6 1
28E 6awv Open in New Window Bound ligand 4 1
28E 6ax0 Open in New Window Bound ligand 2 1