Chemical Components in the PDB

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NAR : Summary

Code

NAR

One-letter code

X

Molecule name

NARINGENIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one
OpenEye OEToolkits 1.5.0 (2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one

Formula

C15 H12 O5

Formal charge

0

Molecular weight

272.253 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C2c3c(OC(c1ccc(O)cc1)C2)cc(O)cc3O
SMILES CACTVS 3.341 Oc1ccc(cc1)[CH]2CC(=O)c3c(O)cc(O)cc3O2
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C2CC(=O)c3c(cc(cc3O2)O)O)O
Canonical SMILES CACTVS 3.341 Oc1ccc(cc1)[C@@H]2CC(=O)c3c(O)cc(O)cc3O2
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[C@@H]2CC(=O)c3c(cc(cc3O2)O)O)O

IUPAC InChI

InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-6,13,16-18H,7H2/t13-/m0/s1

IUPAC InChI key

FTVWIRXFELQLPI-ZDUSSCGKSA-N
NAR

wwPDB Information

Atom count

32 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NAR : Atoms of Molecule

Total Number of Atoms: 32
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 1.816 0.037 -2.129
2 C2 C C2 N Y N 0 1.724 0.139 -3.509
3 C3 C C3 N Y N 0 0.488 0.096 -4.144
4 C4 C C4 N Y N 0 -0.665 -0.038 -3.394
5 C5 C C5 N Y N 0 -0.577 -0.125 -1.995
6 C6 C C6 N Y N 0 0.672 -0.106 -1.354
7 C7 C C7 N N N 0 -1.8 -0.229 -1.186
8 C8 C C8 N N N 0 -1.577 -0.483 0.297
9 C9 C C9 S N N 0 -0.306 0.295 0.672
10 O1 O O1 N N N 0 0.809 -0.243 -0.019
11 O2 O O2 N N N 0 -2.909 -0.12 -1.667
12 C10 C C10 N Y N 0 -0.073 0.188 2.157
13 C11 C C11 N Y N 0 0.691 -0.845 2.663
14 C12 C C12 N Y N 0 0.906 -0.945 4.024
15 C13 C C13 N Y N 0 0.352 -0.006 4.883
16 C14 C C14 N Y N 0 -0.419 1.026 4.373
17 C15 C C15 N Y N 0 -0.626 1.125 3.01
18 O3 O O3 N N N 0 0.562 -0.102 6.222
19 O4 O O4 N N N 0 2.852 0.284 -4.248
20 O5 O O5 N N N 0 -1.874 -0.087 -4.006
21 H11 H 1H1 N N N 0 2.785 0.069 -1.653
22 H31 H 1H3 N N N 0 0.429 0.168 -5.22
23 H81 H 1H8 N N N 0 -1.432 -1.548 0.478
24 H82 H 2H8 N N N 0 -2.426 -0.115 0.873
25 H9 H H9 N N N 0 -0.43 1.343 0.398
26 H111 H 1H11 N N N 0 1.122 -1.575 1.994
27 H121 H 1H12 N N N 0 1.504 -1.752 4.419
28 H141 H 1H14 N N N 0 -0.851 1.759 5.039
29 H151 H 1H15 N N N 0 -1.223 1.932 2.612
30 HO3 H HO3 N N N 0 1.365 0.4 6.416
31 H41 H 1H4 N N N 0 3.015 1.234 -4.326
32 H51 H 1H5 N N N 0 -2.192 0.823 -4.071



NAR : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.39 N Y
2 C1 C6 C C sing 1.39 N Y
3 C1 H11 C H sing 1.08 N N
4 C2 C3 C C sing 1.39 N Y
5 C2 O4 C O sing 1.36 N N
6 C3 C4 C C doub 1.38 N Y
7 C3 H31 C H sing 1.08 N N
8 C4 C5 C C sing 1.4 N Y
9 C4 O5 C O sing 1.36 N N
10 C5 C6 C C doub 1.4 N Y
11 C5 C7 C C sing 1.47 N N
12 C6 O1 C O sing 1.35 N N
13 C7 C8 C C sing 1.52 N N
14 C7 O2 C O doub 1.21 N N
15 C8 C9 C C sing 1.54 N N
16 C8 H81 C H sing 1.09 N N
17 C8 H82 C H sing 1.09 N N
18 C9 O1 C O sing 1.42 N N
19 C9 C10 C C sing 1.51 N N
20 C9 H9 C H sing 1.09 N N
21 C10 C11 C C sing 1.38 N Y
22 C10 C15 C C doub 1.38 N Y
23 C11 C12 C C doub 1.38 N Y
24 C11 H111 C H sing 1.08 N N
25 C12 C13 C C sing 1.39 N Y
26 C12 H121 C H sing 1.08 N N
27 C13 C14 C C doub 1.39 N Y
28 C13 O3 C O sing 1.36 N N
29 C14 C15 C C sing 1.38 N Y
30 C14 H141 C H sing 1.08 N N
31 C15 H151 C H sing 1.08 N N
32 O3 HO3 O H sing 0.97 N N
33 O4 H41 O H sing 0.97 N N
34 O5 H51 O H sing 0.97 N N



NAR : Used in PDB Entries

Total Number of PDB Entries: 22
Ligand Code PDB Entry ID Type Total Distinct
NAR 1cgk Open in New Window Bound ligand 1 1
NAR 1eyq Open in New Window Bound ligand 2 1
NAR 2brt Open in New Window Bound ligand 1 1
NAR 2uxu Open in New Window Bound ligand 2 1
NAR 4a87 Open in New Window Bound ligand 1 1
NAR 4d06 Open in New Window Bound ligand 7 1
NAR 4deu Open in New Window Bound ligand 2 1
NAR 4eh3 Open in New Window Bound ligand 1 1
NAR 5wkr Open in New Window Bound ligand 1 1
NAR 5wks Open in New Window Bound ligand 1 1
NAR 6g8h Open in New Window Bound ligand 1 1
NAR 6ms8 Open in New Window Bound ligand 5 1
NAR 7bur Open in New Window Bound ligand 2 1
NAR 7vez Open in New Window Bound ligand 4 1
NAR 7vf0 Open in New Window Bound ligand 4 1
NAR 7yj7 Open in New Window Bound ligand 1 1
NAR 7yj9 Open in New Window Bound ligand 1 1
NAR 8b35 Open in New Window Bound ligand 2 1
NAR 8feu Open in New Window Bound ligand 2 1
NAR 8few Open in New Window Bound ligand 2 1
NAR 8fio Open in New Window Bound ligand 2 1
NAR 8gkn Open in New Window Bound ligand 2 1