Chemical Components in the PDB

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S09 : Summary

Code

S09

One-letter code

X

Molecule name

(1R,2R)-4-hydroxy-1-[4-(phenylcarbamamido)benzamido]-2,3-dihydro-1H-indene-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2R)-4-hydroxy-1-[4-(phenylcarbamamido)benzamido]-2,3-dihydro-1H-indene-2-carboxylic acid
OpenEye OEToolkits 2.0.7 (1~{R},2~{R})-4-oxidanyl-1-[[4-(phenylcarbamoylamino)phenyl]carbonylamino]-2,3-dihydro-1~{H}-indene-2-carboxylic acid

Formula

C24 H21 N3 O5

Formal charge

0

Molecular weight

431.441 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(Nc1ccccc1)Nc1ccc(cc1)C(=O)NC1c2cccc(O)c2CC1C(=O)O
SMILES CACTVS 3.385 OC(=O)[CH]1Cc2c(O)cccc2[CH]1NC(=O)c3ccc(NC(=O)Nc4ccccc4)cc3
SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)NC(=O)Nc2ccc(cc2)C(=O)NC3c4cccc(c4CC3C(=O)O)O
Canonical SMILES CACTVS 3.385 OC(=O)[C@@H]1Cc2c(O)cccc2[C@@H]1NC(=O)c3ccc(NC(=O)Nc4ccccc4)cc3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)NC(=O)Nc2ccc(cc2)C(=O)N[C@H]3c4cccc(c4C[C@H]3C(=O)O)O

IUPAC InChI

InChI=1S/C24H21N3O5/c28-20-8-4-7-17-18(20)13-19(23(30)31)21(17)27-22(29)14-9-11-16(12-10-14)26-24(32)25-15-5-2-1-3-6-15/h1-12,19,21,28H,13H2,(H,27,29)(H,30,31)(H2,25,26,32)/t19-,21+/m1/s1

IUPAC InChI key

UCQXDGPOPJQAQB-CTNGQTDRSA-N
S09

wwPDB Information

Atom count

53 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-06-23

Last modified at

2022-07-08

Status

Released

Obsoleted

Not Assigned



S09 : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C18 C C1 N Y N 0 -2.438 1.803 -0.002
2 C16 C C2 N Y N 0 -0.417 2.775 -0.85
3 C17 C C3 N Y N 0 -1.751 2.891 -0.53
4 C15 C C4 N Y N 0 0.247 1.562 -0.644
5 C14 C C5 N N N 0 1.677 1.435 -0.985
6 C20 C C9 N N N 0 -4.618 0.874 0.155
7 C12 C C6 R N N 0 3.735 0.138 -1.124
8 C11 C C7 N Y N 0 4.592 0.408 0.094
9 C10 C C8 N Y N 0 4.496 1.398 1.057
10 C02 C C10 N N N 0 3.108 -2.282 -0.878
11 C03 C C11 R N N 0 4.061 -1.314 -1.533
12 C04 C C12 N N N 0 5.492 -1.499 -0.987
13 C05 C C13 N Y N 0 5.601 -0.533 0.173
14 C06 C C14 N Y N 0 6.515 -0.48 1.219
15 C08 C C15 N Y N 0 6.414 0.514 2.18
16 C09 C C16 N Y N 0 5.403 1.452 2.097
17 C22 C C17 N Y N 0 -6.728 -0.169 0.499
18 C23 C C18 N Y N 0 -6.205 -1.436 0.724
19 C24 C C19 N Y N 0 -7.028 -2.543 0.661
20 C25 C C20 N Y N 0 -8.372 -2.392 0.373
21 C26 C C21 N Y N 0 -8.896 -1.133 0.148
22 C27 C C22 N Y N 0 -8.079 -0.021 0.21
23 C29 C C23 N Y N 0 -1.779 0.596 0.21
24 C30 C C24 N Y N 0 -0.445 0.473 -0.108
25 N13 N N1 N N N 0 2.316 0.265 -0.785
26 O28 O O3 N N N 0 -4.211 -0.145 -0.368
27 N19 N N2 N N N 0 -3.789 1.923 0.321
28 N21 N N3 N N N 0 -5.898 0.955 0.568
29 O01 O O1 N N N 0 2.014 -2.695 -1.537
30 O07 O O2 N N N 0 7.508 -1.404 1.299
31 H101 H H4 N N N 0 3.707 2.134 0.994
32 O31 O O4 N N N 0 2.279 2.385 -1.447
33 O32 O O5 N N N 0 3.329 -2.684 0.239
34 H161 H H1 N N N 0 0.116 3.62 -1.26
35 H171 H H2 N N N 0 -2.264 3.827 -0.69
36 H121 H H3 N N N 0 3.994 0.825 -1.93
37 H031 H H5 N N N 0 4.042 -1.425 -2.617
38 H042 H H6 N N N 0 5.635 -2.523 -0.64
39 H041 H H7 N N N 0 6.225 -1.255 -1.755
40 H081 H H8 N N N 0 7.124 0.554 2.993
41 H091 H H9 N N N 0 5.323 2.227 2.845
42 H231 H H10 N N N 0 -5.155 -1.554 0.949
43 H241 H H11 N N N 0 -6.621 -3.528 0.836
44 H251 H H12 N N N 0 -9.013 -3.26 0.324
45 H261 H H13 N N N 0 -9.946 -1.018 -0.077
46 H271 H H14 N N N 0 -8.489 0.962 0.035
47 H291 H H15 N N N 0 -2.314 -0.246 0.624
48 H301 H H16 N N N 0 0.065 -0.466 0.053
49 H131 H H17 N N N 0 1.835 -0.493 -0.417
50 H191 H H18 N N N 0 -4.132 2.763 0.666
51 H211 H H19 N N N 0 -6.245 1.793 0.913
52 H1 H H20 N N N 0 1.433 -3.316 -1.076
53 H071 H H21 N N N 0 8.319 -1.15 0.838



S09 : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C09 C08 C C doub 1.38 N Y
2 C09 C10 C C sing 1.38 N Y
3 C08 C06 C C sing 1.39 N Y
4 C10 C11 C C doub 1.38 N Y
5 C06 O07 C O sing 1.36 N N
6 C06 C05 C C doub 1.39 N Y
7 C11 C05 C C sing 1.38 N Y
8 C11 C12 C C sing 1.51 N N
9 C05 C04 C C sing 1.51 N N
10 C12 C03 C C sing 1.54 N N
11 C12 N13 C N sing 1.46 N N
12 C03 C04 C C sing 1.54 N N
13 C03 C02 C C sing 1.51 N N
14 O31 C14 O C doub 1.22 N N
15 C14 N13 C N sing 1.35 N N
16 C14 C15 C C sing 1.48 N N
17 O32 C02 O C doub 1.21 N N
18 C02 O01 C O sing 1.34 N N
19 C15 C16 C C doub 1.4 N Y
20 C15 C30 C C sing 1.4 N Y
21 C16 C17 C C sing 1.38 N Y
22 C30 C29 C C doub 1.38 N Y
23 C17 C18 C C doub 1.39 N Y
24 C29 C18 C C sing 1.39 N Y
25 C18 N19 C N sing 1.39 N N
26 O28 C20 O C doub 1.22 N N
27 N19 C20 N C sing 1.35 N N
28 C20 N21 C N sing 1.35 N N
29 N21 C22 N C sing 1.4 N N
30 C23 C22 C C doub 1.39 N Y
31 C23 C24 C C sing 1.38 N Y
32 C22 C27 C C sing 1.39 N Y
33 C24 C25 C C doub 1.38 N Y
34 C27 C26 C C doub 1.38 N Y
35 C25 C26 C C sing 1.38 N Y
36 C16 H161 C H sing 1.08 N N
37 C17 H171 C H sing 1.08 N N
38 C12 H121 C H sing 1.09 N N
39 C10 H101 C H sing 1.08 N N
40 C03 H031 C H sing 1.09 N N
41 C04 H042 C H sing 1.09 N N
42 C04 H041 C H sing 1.09 N N
43 C08 H081 C H sing 1.08 N N
44 C09 H091 C H sing 1.08 N N
45 C23 H231 C H sing 1.08 N N
46 C24 H241 C H sing 1.08 N N
47 C25 H251 C H sing 1.08 N N
48 C26 H261 C H sing 1.08 N N
49 C27 H271 C H sing 1.08 N N
50 C29 H291 C H sing 1.08 N N
51 C30 H301 C H sing 1.08 N N
52 N13 H131 N H sing 0.97 N N
53 N19 H191 N H sing 0.97 N N
54 N21 H211 N H sing 0.97 N N
55 O01 H1 O H sing 0.97 N N
56 O07 H071 O H sing 0.97 N N



S09 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
S09 5spb Open in New Window Bound ligand 1 1