Chemical Components in the PDB

pdbe.org/chem
spacer

VSI : Summary

Code

VSI

One-letter code

X

Molecule name

N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(6-cyano-1H-indol-1-yl)acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(6-cyano-1H-indol-1-yl)acetamide
OpenEye OEToolkits 1.7.6 N-[N-[[4-acetamido-3,5-bis(chloranyl)phenyl]methyl]carbamimidoyl]-2-(6-cyanoindol-1-yl)ethanamide

Formula

C21 H18 Cl2 N6 O2

Formal charge

0

Molecular weight

457.313 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Clc1cc(cc(Cl)c1NC(=O)C)CNC(=[N@H])NC(=O)Cn3c2cc(C#N)ccc2cc3
SMILES CACTVS 3.370 CC(=O)Nc1c(Cl)cc(CNC(=N)NC(=O)Cn2ccc3ccc(cc23)C#N)cc1Cl
SMILES OpenEye OEToolkits 1.7.6 CC(=O)Nc1c(cc(cc1Cl)CNC(=N)NC(=O)Cn2ccc3c2cc(cc3)C#N)Cl
Canonical SMILES CACTVS 3.370 CC(=O)Nc1c(Cl)cc(CNC(=N)NC(=O)Cn2ccc3ccc(cc23)C#N)cc1Cl
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C(\NCc1cc(c(c(c1)Cl)NC(=O)C)Cl)/NC(=O)Cn2ccc3c2cc(cc3)C#N

IUPAC InChI

InChI=1S/C21H18Cl2N6O2/c1-12(30)27-20-16(22)6-14(7-17(20)23)10-26-21(25)28-19(31)11-29-5-4-15-3-2-13(9-24)8-18(15)29/h2-8H,10-11H2,1H3,(H,27,30)(H3,25,26,28,31)

IUPAC InChI key

QNSBKNRQYCQXMO-UHFFFAOYSA-N
VSI

wwPDB Information

Atom count

49 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-28

Last modified at

2013-11-08

Status

Released

Obsoleted

Not Assigned



VSI : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 2.68 -2.199 0.0020
2 CA C CA N N N 0 4.081 -2.05 -0.533
3 CAA C CAA N Y N 0 4.863 3.159 -0.449
4 CAB C CAB N Y N 0 4.858 2.282 0.645
5 CAC C CAC N Y N 0 4.634 0.919 0.454
6 CAD C CAD N Y N 0 4.416 0.433 -0.826
7 CAE C CAE N Y N 0 4.424 1.324 -1.918
8 CAF C CAF N Y N 0 4.65 2.689 -1.71
9 CAH C CAH N Y N 0 4.032 -0.762 -2.689
10 CAI C CAI N Y N 0 4.168 0.509 -3.105
11 CAN C CAN N N N 0 1.053 -3.454 1.17
12 CAQ C CAQ N N N 0 -1.261 -2.655 1.406
13 CAR C CAR N Y N 0 -2.107 -1.497 0.944
14 CAS C CAS N Y N 0 -2.185 -0.35 1.712
15 CAT C CAT N Y N 0 -2.956 0.717 1.288
16 CAU C CAU N Y N 0 -3.661 0.631 0.094
17 CAV C CAV N Y N 0 -3.584 -0.525 -0.673
18 CAW C CAW N Y N 0 -2.807 -1.585 -0.245
19 CBA C CBA N N N 0 -5.732 1.513 -0.68
20 CBB C CBB N N N 0 -6.607 2.69 -1.024
21 CBD C CBD N N N 0 5.084 2.788 1.966
22 CLX CL CLX N N N 0 -4.463 -0.637 -2.165
23 CLY CL CLY N N N 0 -3.043 2.161 2.247
24 H1 H H1 N N N 0 -7.093 3.058 -0.12
25 H10 H H10 N N N 0 1.411 -5.162 2.093
26 H11 H H11 N N N 0 3.049 -3.886 1.042
27 H12 H H12 N N N 0 4.784 -1.995 0.298
28 H13 H H13 N N N 0 4.324 -2.91 -1.157
29 H14 H H14 N N N 0 4.63 0.246 1.298
30 H15 H H15 N N N 0 5.037 4.213 -0.291
31 H16 H H16 N N N 0 4.655 3.37 -2.548
32 H17 H H17 N N N 0 4.103 0.862 -4.124
33 H18 H H18 N N N 0 3.84 -1.607 -3.333
34 H2 H H2 N N N 0 -5.997 3.483 -1.457
35 H3 H H3 N N N 0 -7.365 2.381 -1.743
36 H4 H H4 N N N 0 -4.056 2.598 -0.392
37 H5 H H5 N N N 0 -2.747 -2.484 -0.841
38 H6 H H6 N N N 0 -1.636 -0.284 2.64
39 H7 H H7 N N N 0 -1.228 -2.669 2.496
40 H8 H H8 N N N 0 -1.694 -3.588 1.044
41 H9 H H9 N N N 0 0.323 -1.747 0.323
42 N N N N Y N 0 4.172 -0.826 -1.332
43 NAL N NAL N N N 0 2.361 -3.259 0.77
44 NAO N NAO N N N 0 0.098 -2.51 0.879
45 NAP N NAP N N N 0 0.725 -4.531 1.824
46 NAZ N NAZ N N N 0 -4.443 1.709 -0.338
47 NBE N NBE N N N 0 5.263 3.189 3.013
48 O O O N N N 0 1.84 -1.364 -0.258
49 OBC O OBC N N N 0 -6.187 0.389 -0.71



VSI : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NAP CAN N C doub 1.3 N N
2 NAO CAN N C sing 1.37 N N
3 NAO CAQ N C sing 1.46 N N
4 CAN NAL C N sing 1.38 N N
5 CAQ CAR C C sing 1.51 N N
6 CAW CAR C C doub 1.38 N Y
7 CAW CAV C C sing 1.38 N Y
8 O C O C doub 1.21 N N
9 CLX CAV CL C sing 1.74 N N
10 NAL C N C sing 1.35 N N
11 CAR CAS C C sing 1.38 N Y
12 CAV CAU C C doub 1.39 N Y
13 C CA C C sing 1.51 N N
14 CAS CAT C C doub 1.38 N Y
15 CAU CAT C C sing 1.39 N Y
16 CAU NAZ C N sing 1.4 N N
17 CA N C N sing 1.46 N N
18 CAH N C N sing 1.37 N Y
19 CAH CAI C C doub 1.34 N Y
20 N CAD N C sing 1.38 N Y
21 CAT CLY C CL sing 1.74 N N
22 OBC CBA O C doub 1.21 N N
23 NAZ CBA N C sing 1.35 N N
24 CBA CBB C C sing 1.51 N N
25 CAI CAE C C sing 1.46 N Y
26 CAD CAC C C doub 1.39 N Y
27 CAD CAE C C sing 1.41 N Y
28 CAC CAB C C sing 1.39 N Y
29 CAE CAF C C doub 1.4 N Y
30 CAB CAA C C doub 1.4 N Y
31 CAB CBD C C sing 1.43 N N
32 CAF CAA C C sing 1.36 N Y
33 CBD NBE C N trip 1.14 N N
34 CBB H1 C H sing 1.09 N N
35 CBB H2 C H sing 1.09 N N
36 CBB H3 C H sing 1.09 N N
37 NAZ H4 N H sing 0.97 N N
38 CAW H5 C H sing 1.08 N N
39 CAS H6 C H sing 1.08 N N
40 CAQ H7 C H sing 1.09 N N
41 CAQ H8 C H sing 1.09 N N
42 NAO H9 N H sing 0.97 N N
43 NAP H10 N H sing 0.97 N N
44 NAL H11 N H sing 0.97 N N
45 CA H12 C H sing 1.09 N N
46 CA H13 C H sing 1.09 N N
47 CAC H14 C H sing 1.08 N N
48 CAA H15 C H sing 1.08 N N
49 CAF H16 C H sing 1.08 N N
50 CAI H17 C H sing 1.08 N N
51 CAH H18 C H sing 1.08 N N



VSI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VSI 4ivs Open in New Window Bound ligand 1 1