Chemical Components in the PDB

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7I6 : Summary

Code

7I6

One-letter code

X

Molecule name

1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea

Systematic names

ProgramVersionName
ACDLabs 12.01 1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea
OpenEye OEToolkits 1.7.6 1-[(4-aminophenyl)methyl]-3-[(2S)-4-methylsulfanyl-1-[(2R)-2-(2-methylsulfanylphenyl)pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]urea

Formula

C24 H32 N4 O2 S2

Formal charge

0

Molecular weight

472.666 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N2C(c1c(SC)cccc1)CCC2)C(NC(=O)NCc3ccc(N)cc3)CCSC
SMILES CACTVS 3.370 CSCC[CH](NC(=O)NCc1ccc(N)cc1)C(=O)N2CCC[CH]2c3ccccc3SC
SMILES OpenEye OEToolkits 1.7.6 CSCCC(C(=O)N1CCCC1c2ccccc2SC)NC(=O)NCc3ccc(cc3)N
Canonical SMILES CACTVS 3.370 CSCC[C@H](NC(=O)NCc1ccc(N)cc1)C(=O)N2CCC[C@@H]2c3ccccc3SC
Canonical SMILES OpenEye OEToolkits 1.7.6 CSCC[C@@H](C(=O)N1CCC[C@@H]1c2ccccc2SC)NC(=O)NCc3ccc(cc3)N

IUPAC InChI

InChI=1S/C24H32N4O2S2/c1-31-15-13-20(27-24(30)26-16-17-9-11-18(25)12-10-17)23(29)28-14-5-7-21(28)19-6-3-4-8-22(19)32-2/h3-4,6,8-12,20-21H,5,7,13-16,25H2,1-2H3,(H2,26,27,30)/t20-,21+/m0/s1

IUPAC InChI key

SXQHCTVKKRKZEF-LEWJYISDSA-N
7I6

wwPDB Information

Atom count

64 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-15

Last modified at

2014-02-14

Status

Released

Obsoleted

Not Assigned



7I6 : Atoms of Molecule

Total Number of Atoms: 64
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAB C CAB N N N 0 6.924 2.682 -2.03
2 SAW S SAW N N N 0 5.975 1.232 -1.497
3 CBB C CBB N Y N 0 4.907 1.889 -0.259
4 CAH C CAH N Y N 0 4.959 3.241 0.059
5 CAF C CAF N Y N 0 4.121 3.753 1.03
6 CAG C CAG N Y N 0 3.232 2.922 1.686
7 CAI C CAI N Y N 0 3.178 1.576 1.373
8 CBC C CBC N Y N 0 4.008 1.058 0.398
9 CBE C CBE R N N 0 3.944 -0.407 0.053
10 CAQ C CAQ N N N 0 4.985 -1.188 0.883
11 CAN C CAN N N N 0 4.239 -2.504 1.227
12 CAS C CAS N N N 0 2.787 -1.998 1.415
13 NBF N NBF N N N 0 2.619 -0.945 0.398
14 C C C N N N 0 1.446 -0.54 -0.129
15 O O O N N N 0 1.417 0.398 -0.897
16 SD S SD N N N 0 -1.242 -4.922 -0.983
17 CA C CA S N N 0 0.17 -1.254 0.237
18 CB C CB N N N 0 0.081 -2.569 -0.54
19 CG C CG N N N 0 -1.136 -3.363 -0.061
20 CE C CE N N N 0 -2.72 -5.709 -0.285
21 N N N N N N 0 -0.977 -0.408 -0.101
22 CAX C CAX N N N 0 -2.145 -0.565 0.552
23 OAD O OAD N N N 0 -2.247 -1.409 1.422
24 NAT N NAT N N N 0 -3.201 0.214 0.242
25 CAP C CAP N N N 0 -4.471 0.043 0.951
26 CBA C CBA N Y N 0 -5.48 1.028 0.419
27 CAL C CAL N Y N 0 -5.588 2.282 0.991
28 CAJ C CAJ N Y N 0 -6.511 3.187 0.505
29 CAZ C CAZ N Y N 0 -7.332 2.836 -0.559
30 NAC N NAC N N N 0 -8.266 3.749 -1.053
31 CAK C CAK N Y N 0 -7.221 1.575 -1.131
32 CAM C CAM N Y N 0 -6.292 0.677 -0.644
33 H1 H H1 N N N 0 7.629 2.39 -2.809
34 H2 H H2 N N N 0 6.243 3.438 -2.423
35 H3 H H3 N N N 0 7.47 3.092 -1.181
36 H4 H H4 N N N 0 5.654 3.89 -0.453
37 H5 H H5 N N N 0 4.161 4.804 1.277
38 H6 H H6 N N N 0 2.578 3.325 2.445
39 H7 H H7 N N N 0 2.482 0.93 1.888
40 H8 H H8 N N N 0 4.137 -0.546 -1.01
41 H9 H H9 N N N 0 5.875 -1.393 0.289
42 H10 H H10 N N N 0 5.243 -0.642 1.79
43 H11 H H11 N N N 0 4.301 -3.215 0.403
44 H12 H H12 N N N 0 4.623 -2.941 2.149
45 H13 H H13 N N N 0 2.078 -2.808 1.243
46 H14 H H14 N N N 0 2.655 -1.586 2.416
47 H15 H H15 N N N 0 0.165 -1.464 1.307
48 H16 H H16 N N N 0 -0.021 -2.356 -1.605
49 H17 H H17 N N N 0 0.985 -3.153 -0.372
50 H18 H H18 N N N 0 -1.034 -3.577 1.003
51 H19 H H19 N N N 0 -2.04 -2.779 -0.23
52 H20 H H20 N N N 0 -2.579 -5.863 0.785
53 H21 H H21 N N N 0 -3.585 -5.066 -0.448
54 H22 H H22 N N N 0 -2.885 -6.67 -0.773
55 H23 H H23 N N N 0 -0.895 0.265 -0.794
56 H24 H H24 N N N 0 -3.119 0.887 -0.452
57 H25 H H25 N N N 0 -4.839 -0.972 0.8
58 H26 H H26 N N N 0 -4.318 0.219 2.016
59 H27 H H27 N N N 0 -4.949 2.555 1.818
60 H28 H H28 N N N 0 -6.595 4.167 0.952
61 H29 H H29 N N N 0 -8.343 4.629 -0.653
62 H30 H H30 N N N 0 -8.839 3.503 -1.796
63 H31 H H31 N N N 0 -7.858 1.299 -1.958
64 H32 H H32 N N N 0 -6.202 -0.302 -1.091



7I6 : Chemical Bonds

Total Number of Bonds: 66
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAB SAW C S sing 1.81 N N
2 SAW CBB S C sing 1.76 N N
3 CAH CBB C C doub 1.39 N Y
4 CAH CAF C C sing 1.38 N Y
5 CBB CBC C C sing 1.39 N Y
6 CAF CAG C C doub 1.38 N Y
7 SD CG S C sing 1.81 N N
8 SD CE S C sing 1.81 N N
9 CBC CBE C C sing 1.51 N N
10 CBC CAI C C doub 1.38 N Y
11 CBE CAQ C C sing 1.54 N N
12 CBE NBF C N sing 1.47 N N
13 OAD CAX O C doub 1.22 N N
14 CAQ CAN C C sing 1.55 N N
15 CAG CAI C C sing 1.38 N Y
16 CG CB C C sing 1.53 N N
17 CAX N C N sing 1.35 N N
18 CAX NAT C N sing 1.35 N N
19 CA CB C C sing 1.53 N N
20 CA N C N sing 1.46 N N
21 CA C C C sing 1.51 N N
22 NAT CAP N C sing 1.46 N N
23 CAP CBA C C sing 1.51 N N
24 NBF C N C sing 1.35 N N
25 NBF CAS N C sing 1.47 N N
26 CAN CAS C C sing 1.55 N N
27 C O C O doub 1.21 N N
28 CBA CAM C C doub 1.38 N Y
29 CBA CAL C C sing 1.38 N Y
30 CAM CAK C C sing 1.38 N Y
31 CAL CAJ C C doub 1.38 N Y
32 CAK CAZ C C doub 1.39 N Y
33 CAJ CAZ C C sing 1.39 N Y
34 CAZ NAC C N sing 1.4 N N
35 CAB H1 C H sing 1.09 N N
36 CAB H2 C H sing 1.09 N N
37 CAB H3 C H sing 1.09 N N
38 CAH H4 C H sing 1.08 N N
39 CAF H5 C H sing 1.08 N N
40 CAG H6 C H sing 1.08 N N
41 CAI H7 C H sing 1.08 N N
42 CBE H8 C H sing 1.09 N N
43 CAQ H9 C H sing 1.09 N N
44 CAQ H10 C H sing 1.09 N N
45 CAN H11 C H sing 1.09 N N
46 CAN H12 C H sing 1.09 N N
47 CAS H13 C H sing 1.09 N N
48 CAS H14 C H sing 1.09 N N
49 CA H15 C H sing 1.09 N N
50 CB H16 C H sing 1.09 N N
51 CB H17 C H sing 1.09 N N
52 CG H18 C H sing 1.09 N N
53 CG H19 C H sing 1.09 N N
54 CE H20 C H sing 1.09 N N
55 CE H21 C H sing 1.09 N N
56 CE H22 C H sing 1.09 N N
57 N H23 N H sing 0.97 N N
58 NAT H24 N H sing 0.97 N N
59 CAP H25 C H sing 1.09 N N
60 CAP H26 C H sing 1.09 N N
61 CAL H27 C H sing 1.08 N N
62 CAJ H28 C H sing 1.08 N N
63 NAC H29 N H sing 0.97 N N
64 NAC H30 N H sing 0.97 N N
65 CAK H31 C H sing 1.08 N N
66 CAM H32 C H sing 1.08 N N



7I6 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
7I6 4j5c Open in New Window Bound ligand 1 1
7I6 4zsd Open in New Window Bound ligand 1 1