Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

DF3 : Summary

Code

DF3

One-letter code

X

Molecule name

N-[2-(3-{[2-(2,3-dihydro-1,4-benzodioxin-6-ylamino)-2-oxoethyl]sulfanyl}-1H-indol-1-yl)ethyl]-3-(trifluoromethyl)benzamide

Systematic names

ProgramVersionName
ACDLabs 11.02 N-[2-(3-{[2-(2,3-dihydro-1,4-benzodioxin-6-ylamino)-2-oxoethyl]sulfanyl}-1H-indol-1-yl)ethyl]-3-(trifluoromethyl)benzamide
OpenEye OEToolkits 1.6.1 N-[2-[3-[2-(2,3-dihydro-1,4-benzodioxin-6-ylamino)-2-oxo-ethyl]sulfanylindol-1-yl]ethyl]-3-(trifluoromethyl)benzamide

Formula

C28 H24 F3 N3 O4 S

Formal charge

0

Molecular weight

555.568 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 FC(F)(F)c1cccc(c1)C(=O)NCCn5c2ccccc2c(SCC(=O)Nc3ccc4OCCOc4c3)c5
SMILES CACTVS 3.352 FC(F)(F)c1cccc(c1)C(=O)NCCn2cc(SCC(=O)Nc3ccc4OCCOc4c3)c5ccccc25
SMILES OpenEye OEToolkits 1.7.0 c1ccc2c(c1)c(cn2CCNC(=O)c3cccc(c3)C(F)(F)F)SCC(=O)Nc4ccc5c(c4)OCCO5
Canonical SMILES CACTVS 3.352 FC(F)(F)c1cccc(c1)C(=O)NCCn2cc(SCC(=O)Nc3ccc4OCCOc4c3)c5ccccc25
Canonical SMILES OpenEye OEToolkits 1.7.0 c1ccc2c(c1)c(cn2CCNC(=O)c3cccc(c3)C(F)(F)F)SCC(=O)Nc4ccc5c(c4)OCCO5

IUPAC InChI

InChI=1S/C28H24F3N3O4S/c29-28(30,31)19-5-3-4-18(14-19)27(36)32-10-11-34-16-25(21-6-1-2-7-22(21)34)39-17-26(35)33-20-8-9-23-24(15-20)38-13-12-37-23/h1-9,14-16H,10-13,17H2,(H,32,36)(H,33,35)

IUPAC InChI key

BNPQVUSGXCJYEF-UHFFFAOYSA-N
DF3

wwPDB Information

Atom count

63 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-09-04

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DF3 : Atoms of Molecule

Total Number of Atoms: 63
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAA O OAA N N N 0 -5.373 1.329 0.252
2 OAB O OAB N N N 0 4.729 -0.218 1.309
3 FAC F FAC N N N 0 8.392 -3.922 1.367
4 FAD F FAD N N N 0 9.603 -2.015 1.707
5 FAE F FAE N N N 0 10.127 -3.407 -0.027
6 CAF C CAF N Y N 0 7.526 -1.344 -2.344
7 CAG C CAG N Y N 0 0.285 6.174 1.133
8 CAH C CAH N Y N 0 1.591 5.929 0.728
9 CAI C CAI N Y N 0 6.408 -0.728 -1.821
10 CAJ C CAJ N Y N 0 8.389 -2.039 -1.515
11 CAK C CAK N Y N 0 -7.385 -0.086 -0.471
12 CAL C CAL N Y N 0 -8.692 -0.467 -0.234
13 CAM C CAM N Y N 0 -0.691 5.241 0.929
14 CAN C CAN N Y N 0 1.923 4.744 0.109
15 CAO C CAO N Y N 0 -6.67 -2.365 -0.193
16 CAP C CAP N Y N 0 7.023 -1.509 0.379
17 CAQ C CAQ N Y N 0 -0.299 1.976 -0.635
18 CAR C CAR N N N 0 2.925 1.182 -0.126
19 CAS C CAS N N N 0 -10.606 -3.543 0.137
20 CAT C CAT N N N 0 -9.53 -4.346 0.879
21 CAU C CAU N N N 0 2.146 1.876 -1.245
22 CAV C CAV N N N 0 -3.154 0.922 -0.442
23 NAW N NAW N N N 0 4.11 0.53 -0.689
24 NAX N NAX N N N 0 -5.047 -0.649 -0.698
25 OAY O OAY N N N 0 -10.289 -2.152 0.257
26 OAZ O OAZ N N N 0 -8.262 -4.058 0.279
27 SBA S SBA N N N 0 -2.873 2.584 0.228
28 CBB C CBB N N N 0 -4.604 0.55 -0.271
29 CBC C CBC N N N 0 4.952 -0.148 0.116
30 CBD C CBD N Y N 0 -6.371 -1.035 -0.453
31 CBE C CBE N Y N 0 6.148 -0.806 -0.452
32 CBF C CBF N Y N 0 8.137 -2.121 -0.157
33 CBG C CBG N Y N 0 -8.995 -1.796 0.022
34 CBH C CBH N Y N 0 -7.983 -2.748 0.038
35 CBI C CBI N Y N 0 -1.153 2.841 -0.056
36 CBJ C CBJ N Y N 0 -0.375 4.031 0.309
37 CBK C CBK N Y N 0 0.943 3.782 -0.113
38 NBL N NBL N Y N 0 0.961 2.529 -0.682
39 CBM C CBM N N N 0 9.082 -2.88 0.738
40 HAF H HAF N N N 0 7.726 -1.287 -3.404
41 HAG H HAG N N N 0 0.041 7.109 1.616
42 HAH H HAH N N N 0 2.353 6.675 0.899
43 HAI H HAI N N N 0 5.736 -0.185 -2.469
44 HAJ H HAJ N N N 0 9.263 -2.519 -1.93
45 HAK H HAK N N N 0 -7.153 0.948 -0.674
46 HAL H HAL N N N 0 -9.479 0.272 -0.247
47 HAM H HAM N N N 0 -1.704 5.439 1.247
48 HAN H HAN N N N 0 2.941 4.563 -0.202
49 HAO H HAO N N N 0 -5.882 -3.102 -0.18
50 HAP H HAP N N N 0 6.827 -1.573 1.439
51 HAQ H HAQ N N N 0 -0.563 0.999 -1.013
52 HAR H HAR N N N 0 3.234 1.921 0.614
53 HARA H HARA N N N 0 2.29 0.435 0.349
54 HAS H HAS N N N 0 -10.618 -3.827 -0.915
55 HASA H HASA N N N 0 -11.582 -3.738 0.581
56 HAT H HAT N N N 0 -9.513 -4.057 1.929
57 HATA H HATA N N N 0 -9.743 -5.412 0.794
58 HAU H HAU N N N 0 2.781 2.624 -1.72
59 HAUA H HAUA N N N 0 1.837 1.138 -1.985
60 HAV H HAV N N N 0 -2.898 0.909 -1.501
61 HAVA H HAVA N N N 0 -2.529 0.205 0.092
62 HNAW H HNAW N N N 0 4.289 0.586 -1.641
63 HNAX H HNAX N N N 0 -4.449 -1.245 -1.176



DF3 : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAA CBB O C doub 1.21 N N
2 OAB CBC O C doub 1.22 N N
3 CBM FAC C F sing 1.4 N N
4 CBM FAD C F sing 1.4 N N
5 FAE CBM F C sing 1.4 N N
6 CAF CAI C C doub 1.38 N Y
7 CAF CAJ C C sing 1.38 N Y
8 CAF HAF C H sing 1.08 N N
9 CAM CAG C C doub 1.37 N Y
10 CAG CAH C C sing 1.39 N Y
11 CAG HAG C H sing 1.08 N N
12 CAH CAN C C doub 1.38 N Y
13 CAH HAH C H sing 1.08 N N
14 CAI CBE C C sing 1.4 N Y
15 CAI HAI C H sing 1.08 N N
16 CAJ CBF C C doub 1.38 N Y
17 CAJ HAJ C H sing 1.08 N N
18 CAL CAK C C doub 1.38 N Y
19 CAK CBD C C sing 1.39 N Y
20 CAK HAK C H sing 1.08 N N
21 CAL CBG C C sing 1.39 N Y
22 CAL HAL C H sing 1.08 N N
23 CAM CBJ C C sing 1.4 N Y
24 CAM HAM C H sing 1.08 N N
25 CBK CAN C C sing 1.39 N Y
26 CAN HAN C H sing 1.08 N N
27 CBD CAO C C doub 1.39 N Y
28 CBH CAO C C sing 1.39 N Y
29 CAO HAO C H sing 1.08 N N
30 CBE CAP C C doub 1.4 N Y
31 CBF CAP C C sing 1.38 N Y
32 CAP HAP C H sing 1.08 N N
33 CBI CAQ C C doub 1.35 N Y
34 CAQ NBL C N sing 1.38 N Y
35 CAQ HAQ C H sing 1.08 N N
36 NAW CAR N C sing 1.47 N N
37 CAU CAR C C sing 1.53 N N
38 CAR HAR C H sing 1.09 N N
39 CAR HARA C H sing 1.09 N N
40 OAY CAS O C sing 1.43 N N
41 CAS CAT C C sing 1.53 N N
42 CAS HAS C H sing 1.09 N N
43 CAS HASA C H sing 1.09 N N
44 CAT OAZ C O sing 1.43 N N
45 CAT HAT C H sing 1.09 N N
46 CAT HATA C H sing 1.09 N N
47 NBL CAU N C sing 1.47 N N
48 CAU HAU C H sing 1.09 N N
49 CAU HAUA C H sing 1.09 N N
50 CBB CAV C C sing 1.51 N N
51 CAV SBA C S sing 1.81 N N
52 CAV HAV C H sing 1.09 N N
53 CAV HAVA C H sing 1.09 N N
54 CBC NAW C N sing 1.35 N N
55 NAW HNAW N H sing 0.97 N N
56 CBB NAX C N sing 1.35 N N
57 CBD NAX C N sing 1.4 N N
58 NAX HNAX N H sing 0.97 N N
59 OAY CBG O C sing 1.36 N N
60 CBH OAZ C O sing 1.36 N N
61 SBA CBI S C sing 1.76 N N
62 CBE CBC C C sing 1.48 N N
63 CBF CBM C C sing 1.51 N N
64 CBG CBH C C doub 1.39 N Y
65 CBI CBJ C C sing 1.47 N Y
66 CBJ CBK C C doub 1.41 N Y
67 CBK NBL C N sing 1.38 N Y



DF3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DF3 3iw5 Open in New Window Bound ligand 1 1