Chemical Components in the PDB

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SN3 : Summary

Code

SN3

One-letter code

X

Molecule name

(R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE

Synonyms

CHLORODYSINOSIN

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R)-3-({(2S,3R)-1-[(2S,3aR,5S,6S,7aS)-2-{[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]carbamoyl}-5,6-dihydroxyoctahydro-1H-indol-1-yl]-3-chloro-4-methyl-1-oxopentan-2-yl}amino)-2-methoxy-3-oxopropyl hydrogen sulfate (non-preferred name)
OpenEye OEToolkits 1.7.0 [(2R)-3-[[(2S,3R)-1-[(2S,3aR,5S,6S,7aS)-2-[2-(1-carbamimidoyl-2,5-dihydropyrrol-3-yl)ethylcarbamoyl]-5,6-dihydroxy-2,3,3a,4,5,6,7,7a-octahydroindol-1-yl]-3-chloro-4-methyl-1-oxo-pentan-2-yl]amino]-2-methoxy-3-oxo-propyl] hydrogen sulfate

Formula

C26 H43 Cl N6 O10 S

Formal charge

0

Molecular weight

667.172 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S(=O)(O)OCC(OC)C(=O)NC(C(=O)N2C(C(=O)NCCC1=CCN(C(=[N@H])N)C1)CC3CC(O)C(O)CC23)C(Cl)C(C)C
SMILES CACTVS 3.370 CO[CH](CO[S](O)(=O)=O)C(=O)N[CH]([CH](Cl)C(C)C)C(=O)N1[CH]2C[CH](O)[CH](O)C[CH]2C[CH]1C(=O)NCCC3=CCN(C3)C(N)=N
SMILES OpenEye OEToolkits 1.7.0 CC(C)C(C(C(=O)N1C2CC(C(CC2CC1C(=O)NCCC3=CCN(C3)C(=N)N)O)O)NC(=O)C(COS(=O)(=O)O)OC)Cl
Canonical SMILES CACTVS 3.370 CO[C@H](CO[S](O)(=O)=O)C(=O)N[C@H]([C@H](Cl)C(C)C)C(=O)N1[C@H]2C[C@H](O)[C@@H](O)C[C@H]2C[C@H]1C(=O)NCCC3=CCN(C3)C(N)=N
Canonical SMILES OpenEye OEToolkits 1.7.0 [H]/N=C(\N)/N1CC=C(C1)CCNC(=O)[C@@H]2C[C@@H]3C[C@@H]([C@H](C[C@@H]3N2C(=O)[C@@H]([C@@H](C(C)C)Cl)NC(=O)[C@@H](COS(=O)(=O)O)OC)O)O

IUPAC InChI

InChI=1S/C26H43ClN6O10S/c1-13(2)21(27)22(31-24(37)20(42-3)12-43-44(39,40)41)25(38)33-16-10-19(35)18(34)9-15(16)8-17(33)23(36)30-6-4-14-5-7-32(11-14)26(28)29/h5,13,15-22,34-35H,4,6-12H2,1-3H3,(H3,28,29)(H,30,36)(H,31,37)(H,39,40,41)/t15-,16+,17+,18+,19+,20-,21-,22-/m1/s1

IUPAC InChI key

BVKDJAALSHFQTE-WNZJUFNWSA-N
SN3

wwPDB Information

Atom count

87 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-03-29

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



SN3 : Atoms of Molecule

Total Number of Atoms: 87
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 0.301 2.977 -2.658
2 C2 C C2 N N N 0 -0.705 3.402 -1.591
3 C3 C C3 R N N 0 -0.038 4.299 -0.547
4 C4 C C4 S N N 0 1.197 3.604 0.055
5 C5 C C5 N N N 0 2.143 3.068 -0.995
6 C6 C C6 S N N 0 1.413 2.163 -1.988
7 O7 O O7 N N N 0 2.331 1.696 -2.978
8 N8 N N8 N N N 0 0.671 2.559 0.938
9 C9 C C9 S N N 0 -0.674 2.971 1.378
10 C10 C C10 N N N 0 -0.985 4.32 0.692
11 C11 C C11 N N N 0 -1.689 1.938 0.962
12 N12 N N12 N N N 0 -2.998 2.14 1.212
13 C13 C C13 N N N 0 -3.973 1.089 0.908
14 C14 C C14 N N N 0 -5.357 1.52 1.398
15 C15 C C15 N N N 0 -6.359 0.439 1.084
16 C16 C C16 N N N 0 -7.078 0.285 -0.23
17 N17 N N17 N N N 0 -7.956 -0.888 -0.108
18 C18 C C18 N N N 0 -7.744 -1.398 1.254
19 C19 C C19 N N N 0 -6.726 -0.502 1.909
20 C20 C C20 N N N 0 -8.799 -1.4 -1.066
21 N21 N N21 N N N 0 -8.878 -0.83 -2.236
22 O25 O O25 N N N 0 0.834 0.703 2.142
23 N22 N N22 N N N 0 -9.559 -2.512 -0.79
24 O23 O O23 N N N 0 -1.328 0.925 0.401
25 C24 C C24 N N N 0 1.305 1.422 1.287
26 C26 C C26 S N N 0 2.599 1.044 0.613
27 C27 C C27 R N N 0 3.745 1.857 1.218
28 C28 C C28 N N N 0 5.024 1.612 0.414
29 C29 C C29 N N N 0 4.845 2.154 -1.006
30 C30 C C30 N N N 0 6.195 2.329 1.089
31 CL31 CL CL31 N N N 0 3.33 3.611 1.169
32 N32 N N32 N N N 0 2.854 -0.384 0.812
33 C33 C C33 N N N 0 3.624 -1.06 -0.064
34 C34 C C34 R N N 0 3.887 -2.53 0.142
35 O35 O O35 N N N 0 4.815 -2.99 -0.843
36 C36 C C36 N N N 0 5.637 -4.073 -0.405
37 C37 C C37 N N N 0 2.575 -3.306 0.008
38 O38 O O38 N N N 0 2.803 -4.682 0.317
39 S39 S S39 N N N 0 1.559 -5.553 0.215
40 O40 O O40 N N N 0 1.277 -5.766 -1.265
41 O41 O O41 N N N 0 1.914 -6.824 0.742
42 O42 O O42 N N N 0 0.482 -4.776 0.721
43 O43 O O43 N N N 0 4.105 -0.485 -1.017
44 O46 O O46 N N N 0 -0.354 2.173 -3.642
45 H1 H H1 N N N 0 0.729 3.861 -3.131
46 H21 H H21 N N N 0 -1.521 3.947 -2.065
47 H22 H H22 N N N 0 -1.104 2.515 -1.1
48 H3 H H3 N N N 0 0.189 5.292 -0.936
49 H4 H H4 N N N 0 1.734 4.325 0.671
50 H51 H H51 N N N 0 2.588 3.904 -1.535
51 H52 H H52 N N N 0 2.933 2.498 -0.507
52 H6 H H6 N N N 0 0.979 1.314 -1.46
53 HO7 H HO7 N N N 0 1.93 1.128 -3.65
54 H9 H H9 N N N 0 -0.689 3.094 2.461
55 H101 H H101 N N N 0 -0.742 5.154 1.35
56 H102 H H102 N N N 0 -2.029 4.364 0.38
57 HN12 H HN12 N N N 0 -3.295 2.98 1.594
58 H131 H H131 N N N 0 -4.004 0.924 -0.169
59 H132 H H132 N N N 0 -3.68 0.166 1.408
60 H141 H H141 N N N 0 -5.325 1.685 2.475
61 H142 H H142 N N N 0 -5.649 2.443 0.897
62 H161 H H161 N N N 0 -7.674 1.174 -0.433
63 H162 H H162 N N N 0 -6.357 0.126 -1.031
64 H181 H H181 N N N 0 -8.68 -1.37 1.811
65 H182 H H182 N N N 0 -7.363 -2.418 1.213
66 H192 H H192 N N N 0 -6.355 -0.62 2.917
67 HN21 H HN21 N N N 0 -9.473 -1.191 -2.911
68 H221 H H221 N N N 0 -9.5 -2.935 0.081
69 H222 H H222 N N N 0 -10.154 -2.873 -1.465
70 H26 H H26 N N N 0 2.528 1.255 -0.454
71 H27 H H27 N N N 0 3.902 1.55 2.252
72 H28 H H28 N N N 0 5.227 0.542 0.372
73 H291 H H291 N N N 0 4.01 1.643 -1.486
74 H292 H H292 N N N 0 4.641 3.224 -0.964
75 H293 H H293 N N N 0 5.756 1.979 -1.578
76 H301 H H301 N N N 0 6.379 1.883 2.067
77 H302 H H302 N N N 0 7.088 2.228 0.471
78 H303 H H303 N N N 0 5.955 3.385 1.21
79 HN32 H HN32 N N N 0 2.47 -0.844 1.575
80 H34 H H34 N N N 0 4.303 -2.689 1.136
81 H361 H H361 N N N 0 6.218 -3.761 0.463
82 H362 H H362 N N N 0 5.008 -4.921 -0.135
83 H363 H H363 N N N 0 6.314 -4.364 -1.208
84 H371 H H371 N N N 0 1.838 -2.895 0.698
85 H372 H H372 N N N 0 2.204 -3.219 -1.013
86 HO40 H HO40 N N N 0 0.498 -6.311 -1.443
87 HO46 H HO46 N N N 0 0.228 1.868 -4.352



SN3 : Chemical Bonds

Total Number of Bonds: 89
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 C6 C C sing 1.53 N N
3 C1 O46 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 H21 C H sing 1.09 N N
7 C2 H22 C H sing 1.09 N N
8 C3 C4 C C sing 1.54 N N
9 C3 C10 C C sing 1.56 N N
10 C3 H3 C H sing 1.09 N N
11 C4 C5 C C sing 1.51 N N
12 C4 N8 C N sing 1.47 N N
13 C4 H4 C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 H51 C H sing 1.09 N N
16 C5 H52 C H sing 1.09 N N
17 C6 O7 C O sing 1.43 N N
18 C6 H6 C H sing 1.09 N N
19 O7 HO7 O H sing 0.97 N N
20 N8 C9 N C sing 1.47 N N
21 N8 C24 N C sing 1.35 N N
22 C9 C10 C C sing 1.55 N N
23 C9 C11 C C sing 1.51 N N
24 C9 H9 C H sing 1.09 N N
25 C10 H101 C H sing 1.09 N N
26 C10 H102 C H sing 1.09 N N
27 C11 N12 C N sing 1.35 N N
28 C11 O23 C O doub 1.21 N N
29 N12 C13 N C sing 1.47 N N
30 N12 HN12 N H sing 0.97 N N
31 C13 C14 C C sing 1.53 N N
32 C13 H131 C H sing 1.09 N N
33 C13 H132 C H sing 1.09 N N
34 C14 C15 C C sing 1.51 N N
35 C14 H141 C H sing 1.09 N N
36 C14 H142 C H sing 1.09 N N
37 C15 C16 C C sing 1.51 N N
38 C15 C19 C C doub 1.3 N N
39 C16 N17 C N sing 1.47 N N
40 C16 H161 C H sing 1.09 N N
41 C16 H162 C H sing 1.09 N N
42 N17 C18 N C sing 1.47 N N
43 N17 C20 N C sing 1.37 N N
44 C18 C19 C C sing 1.51 N N
45 C18 H181 C H sing 1.09 N N
46 C18 H182 C H sing 1.09 N N
47 C19 H192 C H sing 1.08 N N
48 C20 N21 C N doub 1.3 N N
49 C20 N22 C N sing 1.37 N N
50 N21 HN21 N H sing 0.97 N N
51 N22 H221 N H sing 0.97 N N
52 N22 H222 N H sing 0.97 N N
53 C24 O25 C O doub 1.21 N N
54 C24 C26 C C sing 1.51 N N
55 C26 C27 C C sing 1.53 N N
56 C26 N32 C N sing 1.46 N N
57 C26 H26 C H sing 1.09 N N
58 C27 C28 C C sing 1.53 N N
59 C27 CL31 C CL sing 1.8 N N
60 C27 H27 C H sing 1.09 N N
61 C28 C29 C C sing 1.53 N N
62 C28 C30 C C sing 1.53 N N
63 C28 H28 C H sing 1.09 N N
64 C29 H291 C H sing 1.09 N N
65 C29 H292 C H sing 1.09 N N
66 C29 H293 C H sing 1.09 N N
67 C30 H301 C H sing 1.09 N N
68 C30 H302 C H sing 1.09 N N
69 C30 H303 C H sing 1.09 N N
70 N32 C33 N C sing 1.35 N N
71 N32 HN32 N H sing 0.97 N N
72 C33 C34 C C sing 1.51 N N
73 C33 O43 C O doub 1.21 N N
74 C34 O35 C O sing 1.43 N N
75 C34 C37 C C sing 1.53 N N
76 C34 H34 C H sing 1.09 N N
77 O35 C36 O C sing 1.43 N N
78 C36 H361 C H sing 1.09 N N
79 C36 H362 C H sing 1.09 N N
80 C36 H363 C H sing 1.09 N N
81 C37 O38 C O sing 1.43 N N
82 C37 H371 C H sing 1.09 N N
83 C37 H372 C H sing 1.09 N N
84 O38 S39 O S sing 1.52 N N
85 S39 O40 S O sing 1.52 N N
86 S39 O41 S O doub 1.42 N N
87 S39 O42 S O doub 1.42 N N
88 O40 HO40 O H sing 0.97 N N
89 O46 HO46 O H sing 0.97 N N



SN3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SN3 2gde Open in New Window Bound ligand 1 1