Chemical Components in the PDB

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006 : Summary

Code

006

One-letter code

X

Molecule name

(4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide

Synonyms

KNI-10006

Systematic names

ProgramVersionName
ACDLabs 12.01 (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
OpenEye OEToolkits 1.7.0 (4R)-3-[(2S,3S)-3-[2-(2,6-dimethylphenoxy)ethanoylamino]-2-hydroxy-4-phenyl-butanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide

Formula

C35 H41 N3 O6 S

Formal charge

0

Molecular weight

631.782 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC2c1ccccc1CC2O)C5N(C(=O)C(O)C(NC(=O)COc3c(cccc3C)C)Cc4ccccc4)CSC5(C)C
SMILES CACTVS 3.370 Cc1cccc(C)c1OCC(=O)N[CH](Cc2ccccc2)[CH](O)C(=O)N3CSC(C)(C)[CH]3C(=O)N[CH]4[CH](O)Cc5ccccc45
SMILES OpenEye OEToolkits 1.7.0 Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NC4c5ccccc5CC4O)(C)C)O)C
Canonical SMILES CACTVS 3.370 Cc1cccc(C)c1OCC(=O)N[C@@H](Cc2ccccc2)[C@H](O)C(=O)N3CSC(C)(C)[C@H]3C(=O)N[C@@H]4[C@H](O)Cc5ccccc45
Canonical SMILES OpenEye OEToolkits 1.7.0 Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)N[C@H]4c5ccccc5C[C@H]4O)(C)C)O)C

IUPAC InChI

InChI=1S/C35H41N3O6S/c1-21-11-10-12-22(2)31(21)44-19-28(40)36-26(17-23-13-6-5-7-14-23)30(41)34(43)38-20-45-35(3,4)32(38)33(42)37-29-25-16-9-8-15-24(25)18-27(29)39/h5-16,26-27,29-30,32,39,41H,17-20H2,1-4H3,(H,36,40)(H,37,42)/t26-,27+,29-,30-,32+/m0/s1

IUPAC InChI key

KKTYZYHUPKXLPL-RIQJEONASA-N

Has sub-components

005 , 00B , 00X
006

wwPDB Information

Atom count

86 (45 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-07-03

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



006 : Atoms of Molecule

Total Number of Atoms: 86
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N2 N N2 N N N 0 -2.428 0.132 -1.353
2 C20 C C20 S N N 0 -1.02 0.199 -0.951
3 O20 O O20 N N N 0 -0.265 -0.064 -3.231
4 C21 C C21 N N N 0 -0.514 -1.21 -0.633
5 O21 O O21 N N N 0 2.066 0.111 -2.015
6 C22 C C22 N Y N 0 -1.247 -1.748 0.568
7 C23 C C23 N Y N 0 -2.421 -2.459 0.4
8 C24 C C24 N Y N 0 -3.094 -2.952 1.503
9 C25 C C25 N Y N 0 -2.593 -2.736 2.772
10 C26 C C26 N Y N 0 -1.419 -2.026 2.94
11 C27 C C27 N Y N 0 -0.743 -1.537 1.838
12 C28 C C28 S N N 0 -0.192 0.794 -2.091
13 C29 C C29 N N N 0 1.244 0.925 -1.652
14 N30 N N30 N N N 0 4.851 0.705 0.24
15 O30 O O30 N N N 0 7.473 0.683 0.52
16 C31 C C31 S N N 0 5.362 -0.491 0.915
17 C32 C C32 N Y N 0 5.414 -1.657 -0.049
18 C33 C C33 N Y N 0 4.491 -2.088 -0.987
19 C34 C C34 N Y N 0 4.759 -3.195 -1.768
20 C35 C C35 R N N 0 6.822 -0.271 1.362
21 C36 C C36 N Y N 0 6.608 -2.336 0.104
22 C37 C C37 N Y N 0 6.875 -3.446 -0.68
23 C38 C C38 N Y N 0 5.952 -3.875 -1.615
24 C39 C C39 N N N 0 7.439 -1.674 1.182
25 C40 C C40 N Y N 0 -9.751 -0.087 -0.269
26 O40 O O40 N N N 0 -3.104 0.191 0.759
27 C41 C C41 N Y N 0 -9.026 -1.255 -0.121
28 O41 O O41 N N N 0 -5.674 0.083 0.334
29 C42 C C42 N Y N 0 -7.661 -1.201 0.08
30 C43 C C43 N N N 0 -6.871 -2.474 0.241
31 C44 C C44 N N N 0 -7.051 2.533 0.045
32 C45 C C45 N Y N 0 -7.017 0.027 0.135
33 C46 C C46 N Y N 0 -7.747 1.197 -0.014
34 C47 C C47 N Y N 0 -9.112 1.138 -0.215
35 C48 C C48 N N N 0 -3.397 0.135 -0.416
36 C49 C C49 N N N 0 -4.845 0.067 -0.83
37 C50 C C50 N N N 0 0.645 2.915 -0.306
38 N50 N N50 N N N 0 1.615 1.949 -0.857
39 O50 O O50 N N N 0 2.757 0.182 0.752
40 S50 S S50 N N N 0 1.5 3.528 1.204
41 C51 C C51 N N N 0 3.18 3.396 0.459
42 C52 C C52 N N N 0 3.53 4.656 -0.335
43 C53 C C53 N N N 0 4.235 3.112 1.53
44 C54 C C54 R N N 0 3.001 2.181 -0.479
45 C55 C C55 N N N 0 3.526 0.951 0.215
46 HN2 H HN2 N N N 0 -2.662 0.091 -2.293
47 H20 H H20 N N N 0 -0.925 0.827 -0.065
48 HO20 H HO20 N N N 0 0.068 -0.958 -3.073
49 H21 H H21 N N N 0 -0.691 -1.861 -1.489
50 H21A H H21A N N N 0 0.554 -1.172 -0.42
51 H23 H H23 N N N 0 -2.813 -2.628 -0.592
52 H24 H H24 N N N 0 -4.011 -3.507 1.371
53 H25 H H25 N N N 0 -3.118 -3.121 3.634
54 H26 H H26 N N N 0 -1.027 -1.856 3.932
55 H27 H H27 N N N 0 0.175 -0.982 1.969
56 H28 H H28 N N N 0 -0.584 1.777 -2.35
57 HN30 H HN30 N N N 0 5.466 1.319 -0.189
58 HO30 H HO30 N N N 0 8.394 0.856 0.76
59 H31 H H31 N N N 0 4.736 -0.736 1.773
60 H33 H H33 N N N 0 3.558 -1.558 -1.107
61 H34 H H34 N N N 0 4.036 -3.529 -2.498
62 H35 H H35 N N N 0 6.865 0.043 2.405
63 H37 H H37 N N N 0 7.808 -3.977 -0.561
64 H38 H H38 N N N 0 6.164 -4.741 -2.225
65 H39 H H39 N N N 0 8.478 -1.592 0.861
66 H39A H H39A N N N 0 7.373 -2.239 2.111
67 H40 H H40 N N N 0 -10.818 -0.132 -0.431
68 H41 H H41 N N N 0 -9.528 -2.211 -0.164
69 H43 H H43 N N N 0 -6.529 -2.816 -0.736
70 H43A H H43A N N N 0 -6.01 -2.289 0.883
71 H43B H H43B N N N 0 -7.503 -3.239 0.693
72 H44 H H44 N N N 0 -6.731 2.82 -0.956
73 H44A H H44A N N N 0 -7.737 3.283 0.437
74 H44B H H44B N N N 0 -6.18 2.46 0.698
75 H47 H H47 N N N 0 -9.681 2.049 -0.331
76 H49 H H49 N N N 0 -5.02 -0.853 -1.388
77 H49A H H49A N N N 0 -5.083 0.924 -1.459
78 H50 H H50 N N N 0 0.469 3.729 -1.009
79 H50A H H50A N N N 0 -0.291 2.419 -0.049
80 H52 H H52 N N N 0 3.535 5.517 0.334
81 H52A H H52A N N N 0 4.516 4.54 -0.784
82 H52B H H52B N N N 0 2.789 4.809 -1.119
83 H53 H H53 N N N 0 3.986 2.187 2.049
84 H53A H H53A N N N 0 5.213 3.013 1.059
85 H53B H H53B N N N 0 4.258 3.935 2.245
86 H54 H H54 N N N 0 3.587 2.346 -1.383



006 : Chemical Bonds

Total Number of Bonds: 90
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2 C48 N C sing 1.35 N N
2 N2 C20 N C sing 1.47 N N
3 N2 HN2 N H sing 0.97 N N
4 C21 C20 C C sing 1.53 N N
5 C20 C28 C C sing 1.53 N N
6 C20 H20 C H sing 1.09 N N
7 C28 O20 C O sing 1.43 N N
8 O20 HO20 O H sing 0.97 N N
9 C22 C21 C C sing 1.51 N N
10 C21 H21 C H sing 1.09 N N
11 C21 H21A C H sing 1.09 N N
12 C29 O21 C O doub 1.21 N N
13 C27 C22 C C doub 1.38 N Y
14 C22 C23 C C sing 1.38 N Y
15 C24 C23 C C doub 1.38 N Y
16 C23 H23 C H sing 1.08 N N
17 C25 C24 C C sing 1.38 N Y
18 C24 H24 C H sing 1.08 N N
19 C26 C25 C C doub 1.38 N Y
20 C25 H25 C H sing 1.08 N N
21 C26 C27 C C sing 1.38 N Y
22 C26 H26 C H sing 1.08 N N
23 C27 H27 C H sing 1.08 N N
24 C29 C28 C C sing 1.51 N N
25 C28 H28 C H sing 1.09 N N
26 N50 C29 N C sing 1.35 N N
27 N30 C31 N C sing 1.47 N N
28 N30 C55 N C sing 1.35 N N
29 N30 HN30 N H sing 0.97 N N
30 C35 O30 C O sing 1.43 N N
31 O30 HO30 O H sing 0.97 N N
32 C32 C31 C C sing 1.51 N N
33 C31 C35 C C sing 1.54 N N
34 C31 H31 C H sing 1.09 N N
35 C33 C32 C C doub 1.38 N Y
36 C32 C36 C C sing 1.38 N Y
37 C34 C33 C C sing 1.38 N Y
38 C33 H33 C H sing 1.08 N N
39 C34 C38 C C doub 1.38 N Y
40 C34 H34 C H sing 1.08 N N
41 C39 C35 C C sing 1.54 N N
42 C35 H35 C H sing 1.09 N N
43 C37 C36 C C doub 1.38 N Y
44 C36 C39 C C sing 1.51 N N
45 C38 C37 C C sing 1.38 N Y
46 C37 H37 C H sing 1.08 N N
47 C38 H38 C H sing 1.08 N N
48 C39 H39 C H sing 1.09 N N
49 C39 H39A C H sing 1.09 N N
50 C40 C47 C C doub 1.38 N Y
51 C40 C41 C C sing 1.38 N Y
52 C40 H40 C H sing 1.08 N N
53 C48 O40 C O doub 1.21 N N
54 C41 C42 C C doub 1.38 N Y
55 C41 H41 C H sing 1.08 N N
56 C45 O41 C O sing 1.36 N N
57 O41 C49 O C sing 1.43 N N
58 C42 C45 C C sing 1.39 N Y
59 C42 C43 C C sing 1.51 N N
60 C43 H43 C H sing 1.09 N N
61 C43 H43A C H sing 1.09 N N
62 C43 H43B C H sing 1.09 N N
63 C46 C44 C C sing 1.51 N N
64 C44 H44 C H sing 1.09 N N
65 C44 H44A C H sing 1.09 N N
66 C44 H44B C H sing 1.09 N N
67 C46 C45 C C doub 1.39 N Y
68 C47 C46 C C sing 1.38 N Y
69 C47 H47 C H sing 1.08 N N
70 C49 C48 C C sing 1.51 N N
71 C49 H49 C H sing 1.09 N N
72 C49 H49A C H sing 1.09 N N
73 S50 C50 S C sing 1.84 N N
74 C50 N50 C N sing 1.48 N N
75 C50 H50 C H sing 1.09 N N
76 C50 H50A C H sing 1.09 N N
77 C54 N50 C N sing 1.46 N N
78 O50 C55 O C doub 1.21 N N
79 C51 S50 C S sing 1.84 N N
80 C53 C51 C C sing 1.53 N N
81 C51 C54 C C sing 1.55 N N
82 C51 C52 C C sing 1.53 N N
83 C52 H52 C H sing 1.09 N N
84 C52 H52A C H sing 1.09 N N
85 C52 H52B C H sing 1.09 N N
86 C53 H53 C H sing 1.09 N N
87 C53 H53A C H sing 1.09 N N
88 C53 H53B C H sing 1.09 N N
89 C55 C54 C C sing 1.51 N N
90 C54 H54 C H sing 1.09 N N



006 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
006 3fnu Open in New Window Bound ligand 4 1
006 3kdb Open in New Window Bound ligand 1 1
006 3qs1 Open in New Window Bound ligand 4 1