Chemical Components in the PDB

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KDH : Summary

Code

KDH

One-letter code

X

Molecule name

(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate
OpenEye OEToolkits 1.5.0 [(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)chroman-3-yl] 3,4,5-trihydroxybenzoate

Formula

C22 H18 O11

Formal charge

0

Molecular weight

458.372 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OC2Cc3c(OC2c1cc(O)c(O)c(O)c1)cc(O)cc3O)c4cc(O)c(O)c(O)c4
SMILES CACTVS 3.341 Oc1cc(O)c2C[CH](OC(=O)c3cc(O)c(O)c(O)c3)[CH](Oc2c1)c4cc(O)c(O)c(O)c4
SMILES OpenEye OEToolkits 1.5.0 c1c(cc(c(c1O)O)O)C2C(Cc3c(cc(cc3O2)O)O)OC(=O)c4cc(c(c(c4)O)O)O
Canonical SMILES CACTVS 3.341 Oc1cc(O)c2C[C@@H](OC(=O)c3cc(O)c(O)c(O)c3)[C@H](Oc2c1)c4cc(O)c(O)c(O)c4
Canonical SMILES OpenEye OEToolkits 1.5.0 c1c(cc(c(c1O)O)O)[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)O)OC(=O)c4cc(c(c(c4)O)O)O

IUPAC InChI

InChI=1S/C22H18O11/c23-10-5-12(24)11-7-18(33-22(31)9-3-15(27)20(30)16(28)4-9)21(32-17(11)6-10)8-1-13(25)19(29)14(26)2-8/h1-6,18,21,23-30H,7H2/t18-,21-/m1/s1

IUPAC InChI key

WMBWREPUVVBILR-WIYYLYMNSA-N
KDH

wwPDB Information

Atom count

51 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-01-13

Last modified at

2020-05-27

Status

Released

Obsoleted

Not Assigned



KDH : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N 0 1.154 3.389 -2.301
2 C3 C C3 N Y N 0 0.308 3.424 -1.236
3 C6 C C6 N Y N 0 0.173 4.59 -0.493
4 O7 O O7 N N N 0 0.887 5.7 -0.827
5 C9 C C9 N Y N 0 -0.693 4.621 0.594
6 O10 O O10 N N N 0 -0.829 5.76 1.324
7 C12 C C12 N Y N 0 -1.419 3.488 0.931
8 C14 C C14 N Y N 0 -1.282 2.33 0.189
9 C15 C C15 R N N 0 -2.072 1.102 0.56
10 C20 C C20 N Y N 0 -2.932 -0.871 -0.473
11 C21 C C21 N Y N 0 -3.603 -1.443 -1.549
12 C24 C C24 N Y N 0 -4.135 -2.717 -1.442
13 C26 C C26 N Y N 0 -3.997 -3.427 -0.259
14 C29 C C29 N Y N 0 -3.33 -2.858 0.813
15 C31 C C31 N Y N 0 -2.799 -1.578 0.709
16 C33 C C33 R N N 0 -1.222 0.191 1.455
17 C36 C C36 N N N 0 1.043 -0.559 1.409
18 C38 C C38 N Y N 0 2.246 -1.059 0.717
19 C39 C C39 N Y N 0 3.409 -1.331 1.443
20 C41 C C41 N Y N 0 2.223 -1.268 -0.664
21 C01 C C01 N N N 0 -2.089 -0.988 1.901
22 O01 O O01 N N N 0 -2.417 0.378 -0.622
23 O02 O O02 N N N 0 -4.79 -3.271 -2.496
24 O03 O O03 N N N 0 -3.196 -3.554 1.973
25 C4 C C4 N Y N 0 -0.425 2.298 -0.895
26 O35 O O35 N N N 0 -0.077 -0.298 0.708
27 O37 O O37 N N N 0 1.063 -0.384 2.611
28 C43 C C43 N Y N 0 3.351 -1.737 -1.31
29 O44 O O44 N N N 0 3.33 -1.939 -2.655
30 C46 C C46 N Y N 0 4.511 -2.001 -0.586
31 O47 O O47 N N N 0 5.619 -2.462 -1.223
32 C49 C C49 N Y N 0 4.535 -1.8 0.792
33 O50 O O50 N N N 0 5.667 -2.064 1.498
34 HO1 H HO1 N N N 0 2.055 3.117 -2.078
35 H21 H H21 N N N 0 -3.711 -0.89 -2.47
36 H33 H H33 N N N 0 -0.882 0.748 2.328
37 H4 H H4 N N N 0 -0.324 1.392 -1.475
38 HO7 H HO7 N N N 0 0.437 6.282 -1.454
39 H01 H H01 N N N 0 -2.826 -0.643 2.627
40 H01A H H01A N N N 0 -1.458 -1.749 2.361
41 HO03 H HO03 N N N 0 -2.396 -4.096 2.016
42 HO10 H HO10 N N N 0 -1.525 6.351 1.005
43 H12 H H12 N N N 0 -2.092 3.511 1.776
44 H15 H H15 N N N 0 -2.979 1.395 1.089
45 H26 H H26 N N N 0 -4.41 -4.422 -0.174
46 H39 H H39 N N N 0 3.429 -1.174 2.511
47 H41 H H41 N N N 0 1.324 -1.063 -1.227
48 HO02 H HO02 N N N 0 -4.22 -3.773 -3.095
49 HO44 H HO44 N N N 0 3.595 -1.167 -3.173
50 HO47 H HO47 N N N 0 6.21 -1.765 -1.537
51 HO50 H HO50 N N N 0 5.721 -2.971 1.828



KDH : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C3 O C sing 1.36 N N
2 O1 HO1 O H sing 0.97 N N
3 C3 C6 C C doub 1.39 N Y
4 C3 C4 C C sing 1.39 N Y
5 C6 O7 C O sing 1.36 N N
6 C6 C9 C C sing 1.39 N Y
7 O7 HO7 O H sing 0.97 N N
8 C9 O10 C O sing 1.36 N N
9 C9 C12 C C doub 1.39 N Y
10 O10 HO10 O H sing 0.97 N N
11 C12 C14 C C sing 1.38 N Y
12 C12 H12 C H sing 1.08 N N
13 C14 C15 C C sing 1.51 N N
14 C14 C4 C C doub 1.38 N Y
15 C15 C33 C C sing 1.53 N N
16 C15 O01 C O sing 1.43 N N
17 C15 H15 C H sing 1.09 N N
18 C20 C21 C C doub 1.39 N Y
19 C20 C31 C C sing 1.38 N Y
20 C20 O01 C O sing 1.36 N N
21 C21 C24 C C sing 1.38 N Y
22 C21 H21 C H sing 1.08 N N
23 C24 C26 C C doub 1.39 N Y
24 C24 O02 C O sing 1.36 N N
25 C26 C29 C C sing 1.38 N Y
26 C26 H26 C H sing 1.08 N N
27 C29 C31 C C doub 1.39 N Y
28 C29 O03 C O sing 1.36 N N
29 C31 C01 C C sing 1.51 N N
30 C33 C01 C C sing 1.53 N N
31 C33 O35 C O sing 1.45 N N
32 C33 H33 C H sing 1.09 N N
33 C36 C38 C C sing 1.48 N N
34 C36 O35 C O sing 1.35 N N
35 C36 O37 C O doub 1.21 N N
36 C38 C39 C C doub 1.4 N Y
37 C38 C41 C C sing 1.4 N Y
38 C39 C49 C C sing 1.38 N Y
39 C39 H39 C H sing 1.08 N N
40 C41 C43 C C doub 1.38 N Y
41 C41 H41 C H sing 1.08 N N
42 C01 H01 C H sing 1.09 N N
43 C01 H01A C H sing 1.09 N N
44 O02 HO02 O H sing 0.97 N N
45 O03 HO03 O H sing 0.97 N N
46 C4 H4 C H sing 1.08 N N
47 C43 O44 C O sing 1.36 N N
48 C43 C46 C C sing 1.39 N Y
49 O44 HO44 O H sing 0.97 N N
50 C46 O47 C O sing 1.36 N N
51 C46 C49 C C doub 1.39 N Y
52 O47 HO47 O H sing 0.97 N N
53 C49 O50 C O sing 1.36 N N
54 O50 HO50 O H sing 0.97 N N



KDH : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
KDH 2kdh Open in New Window Bound ligand 1 1
KDH 3ng5 Open in New Window Bound ligand 3 1
KDH 3oob Open in New Window Bound ligand 2 1
KDH 4awm Open in New Window Bound ligand 2 1
KDH 6s2g Open in New Window Bound ligand 14 1
KDH 7upg Open in New Window Bound ligand 10 1
KDH 8qmu Open in New Window Bound ligand 1 1
KDH 8r53 Open in New Window Bound ligand 1 1
KDH 8r6v Open in New Window Bound ligand 1 1