Chemical Components in the PDB

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VKP : Summary

Code

VKP

One-letter code

X

Molecule name

6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine
OpenEye OEToolkits 2.0.7 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine

Formula

C16 H19 Cl2 N5 S

Formal charge

0

Molecular weight

384.327 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c2(Sc1c(c(ccc1)Cl)Cl)ncc(nc2N)N3CCC(N)(CC3)C
SMILES CACTVS 3.385 CC1(N)CCN(CC1)c2cnc(Sc3cccc(Cl)c3Cl)c(N)n2
SMILES OpenEye OEToolkits 2.0.7 CC1(CCN(CC1)c2cnc(c(n2)N)Sc3cccc(c3Cl)Cl)N
Canonical SMILES CACTVS 3.385 CC1(N)CCN(CC1)c2cnc(Sc3cccc(Cl)c3Cl)c(N)n2
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1(CCN(CC1)c2cnc(c(n2)N)Sc3cccc(c3Cl)Cl)N

IUPAC InChI

InChI=1S/C16H19Cl2N5S/c1-16(20)5-7-23(8-6-16)12-9-21-15(14(19)22-12)24-11-4-2-3-10(17)13(11)18/h2-4,9H,5-8,20H2,1H3,(H2,19,22)

IUPAC InChI key

VPEZYDNNURIHBQ-UHFFFAOYSA-N
VKP

wwPDB Information

Atom count

43 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-08-24

Last modified at

2020-09-18

Status

Released

Obsoleted

Not Assigned



VKP : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -0.53 -1.51 -0.038
2 C2 C C2 N Y N 0 0.827 0.09 -0.964
3 C3 C C3 N Y N 0 1.946 -0.565 -0.47
4 C11 C C4 N Y N 0 -3.197 -0.922 -0.419
5 C12 C C5 N Y N 0 -3.82 -1.138 -1.642
6 C13 C C6 N Y N 0 -4.648 -0.169 -2.175
7 C14 C C7 N Y N 0 -4.857 1.016 -1.493
8 C15 C C8 N Y N 0 -4.239 1.236 -0.275
9 C16 C C9 N Y N 0 -3.413 0.267 0.267
10 N1 N N1 N Y N 0 -0.382 -0.395 -0.738
11 N2 N N2 N Y N 0 1.806 -1.682 0.237
12 C4 C C10 N Y N 0 0.596 -2.172 0.466
13 N3 N N3 N N N 0 0.446 -3.34 1.206
14 N4 N N4 N N N 0 3.218 -0.049 -0.711
15 C5 C C11 N N N 0 4.253 -0.895 -0.102
16 C6 C C12 N N N 0 5.636 -0.382 -0.507
17 C7 C C13 N N N 0 5.795 1.068 -0.041
18 C8 C C14 N N N 0 4.677 1.918 -0.65
19 C9 C C15 N N N 0 3.321 1.338 -0.241
20 C10 C C16 N N N 0 7.153 1.606 -0.495
21 N5 N N5 N N N 0 5.71 1.124 1.425
22 S1 S S1 N N N 0 -2.141 -2.156 0.264
23 CL1 CL CL1 N N N 0 -2.643 0.539 1.799
24 CL2 CL CL2 N N N 0 -4.505 2.725 0.577
25 H1 H H1 N N N 0 0.945 1.0 -1.535
26 H2 H H2 N N N 0 -3.657 -2.062 -2.176
27 H3 H H3 N N N 0 -5.132 -0.337 -3.126
28 H4 H H4 N N N 0 -5.504 1.772 -1.913
29 H6 H H6 N N N 0 -0.44 -3.698 1.373
30 H5 H H5 N N N 0 1.227 -3.798 1.555
31 H7 H H7 N N N 0 4.157 -0.861 0.984
32 H8 H H8 N N N 0 4.131 -1.922 -0.445
33 H9 H H9 N N N 0 6.404 -1.0 -0.043
34 H10 H H10 N N N 0 5.738 -0.429 -1.592
35 H11 H H11 N N N 0 4.759 2.942 -0.288
36 H12 H H12 N N N 0 4.764 1.908 -1.737
37 H13 H H13 N N N 0 2.523 1.932 -0.685
38 H14 H H14 N N N 0 3.229 1.361 0.845
39 H16 H H16 N N N 0 7.215 1.564 -1.582
40 H15 H H15 N N N 0 7.948 0.998 -0.062
41 H17 H H17 N N N 0 7.264 2.638 -0.164
42 H18 H H18 N N N 0 5.812 2.071 1.757
43 H19 H H19 N N N 0 4.847 0.716 1.753



VKP : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 C7 C C sing 1.53 N N
2 C9 C8 C C sing 1.53 N N
3 C9 N4 C N sing 1.47 N N
4 C8 C7 C C sing 1.53 N N
5 C7 N5 C N sing 1.47 N N
6 C7 C6 C C sing 1.53 N N
7 C5 N4 C N sing 1.47 N N
8 C5 C6 C C sing 1.53 N N
9 N4 C3 N C sing 1.39 N N
10 C3 C2 C C doub 1.39 N Y
11 C3 N2 C N sing 1.33 N Y
12 C2 N1 C N sing 1.32 N Y
13 C13 C12 C C doub 1.38 N Y
14 C13 C14 C C sing 1.38 N Y
15 N2 C4 N C doub 1.33 N Y
16 C12 C11 C C sing 1.39 N Y
17 N1 C1 N C doub 1.32 N Y
18 C14 C15 C C doub 1.38 N Y
19 C4 C1 C C sing 1.4 N Y
20 C4 N3 C N sing 1.39 N N
21 C1 S1 C S sing 1.76 N N
22 C11 S1 C S sing 1.76 N N
23 C11 C16 C C doub 1.39 N Y
24 C15 C16 C C sing 1.38 N Y
25 C15 CL2 C CL sing 1.74 N N
26 C16 CL1 C CL sing 1.74 N N
27 C2 H1 C H sing 1.08 N N
28 C12 H2 C H sing 1.08 N N
29 C13 H3 C H sing 1.08 N N
30 C14 H4 C H sing 1.08 N N
31 N3 H5 N H sing 0.97 N N
32 N3 H6 N H sing 0.97 N N
33 C5 H7 C H sing 1.09 N N
34 C5 H8 C H sing 1.09 N N
35 C6 H9 C H sing 1.09 N N
36 C6 H10 C H sing 1.09 N N
37 C8 H11 C H sing 1.09 N N
38 C8 H12 C H sing 1.09 N N
39 C9 H13 C H sing 1.09 N N
40 C9 H14 C H sing 1.09 N N
41 C10 H15 C H sing 1.09 N N
42 C10 H16 C H sing 1.09 N N
43 C10 H17 C H sing 1.09 N N
44 N5 H18 N H sing 1.01 N N
45 N5 H19 N H sing 1.01 N N



VKP : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VKP 7jvn Open in New Window Bound ligand 2 1