Chemical Components in the PDB

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LQ6 : Summary

Code

LQ6

One-letter code

X

Molecule name

(2~{S})-4-[[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-6-yl]carbonyl]-1-(3,4-dichlorophenyl)-~{N}-(thiophen-2-ylmethyl)piperazine-2-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{S})-4-[[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-6-yl]carbonyl]-1-(3,4-dichlorophenyl)-~{N}-(thiophen-2-ylmethyl)piperazine-2-carboxamide

Formula

C21 H19 Cl2 N5 O4 S

Formal charge

0

Molecular weight

508.378 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Clc1ccc(cc1Cl)N2CCN(C[CH]2C(=O)NCc3sccc3)C(=O)C4=CC(=O)NC(=O)N4
SMILES OpenEye OEToolkits 2.0.7 c1cc(sc1)CNC(=O)C2CN(CCN2c3ccc(c(c3)Cl)Cl)C(=O)C4=CC(=O)NC(=O)N4
Canonical SMILES CACTVS 3.385 Clc1ccc(cc1Cl)N2CCN(C[C@H]2C(=O)NCc3sccc3)C(=O)C4=CC(=O)NC(=O)N4
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(sc1)CNC(=O)[C@@H]2CN(CCN2c3ccc(c(c3)Cl)Cl)C(=O)C4=CC(=O)NC(=O)N4

IUPAC InChI

InChI=1S/C21H19Cl2N5O4S/c22-14-4-3-12(8-15(14)23)28-6-5-27(20(31)16-9-18(29)26-21(32)25-16)11-17(28)19(30)24-10-13-2-1-7-33-13/h1-4,7-9,17H,5-6,10-11H2,(H,24,30)(H2,25,26,29,32)/t17-/m0/s1

IUPAC InChI key

PBLOKSLGZKWIQI-KRWDZBQOSA-N
LQ6

wwPDB Information

Atom count

52 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-07-07

Last modified at

2022-09-23

Status

Released

Obsoleted

Not Assigned



LQ6 : Atoms of Molecule

Total Number of Atoms: 52
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 2.202 -0.739 0.853
2 N3 N N2 N N N 0 4.65 -0.21 -1.325
3 C4 C C1 N Y N 0 -0.927 1.95 0.953
4 C13 C C7 N Y N 0 -3.7 -5.968 -0.08
5 C5 C C2 N N N 0 1.402 1.563 0.856
6 C6 C C3 N N N 0 2.497 0.613 1.35
7 C7 C C4 N N N 0 0.856 -1.287 1.081
8 C8 C C5 S N N 0 -0.175 -0.261 0.598
9 C10 C C6 N N N 0 -3.366 -2.362 0.833
10 C15 C C8 N N N 0 3.138 -1.456 0.199
11 C17 C C9 N N N 0 5.831 0.353 -1.629
12 C20 C C10 N Y N 0 -1.251 2.237 -0.366
13 N N N3 N N N 0 0.087 1.033 1.241
14 C C C11 N Y N 0 -2.251 3.149 -0.648
15 O O O1 N N N 0 -2.261 -0.054 1.681
16 C1 C C12 N Y N 0 -2.928 3.776 0.384
17 C11 C C13 N Y N 0 -3.633 -3.691 0.175
18 C12 C C14 N Y N 0 -3.367 -4.883 0.712
19 C14 C C15 N Y N 0 -4.232 -5.657 -1.264
20 C16 C C16 N N N 0 4.452 -0.845 -0.118
21 C18 C C17 N N N 0 5.471 -0.906 0.778
22 C19 C C18 N N N 0 6.753 -0.288 0.421
23 C2 C C19 N Y N 0 -2.606 3.492 1.699
24 C3 C C20 N Y N 0 -1.608 2.581 1.986
25 O1 O O2 N N N 0 5.964 0.904 -2.705
26 C9 C C21 N N N 0 -1.56 -0.732 0.959
27 N2 N N4 N N N 0 -2.02 -1.905 0.481
28 N4 N N5 N N N 0 6.869 0.325 -0.775
29 O2 O O3 N N N 0 7.693 -0.32 1.194
30 O3 O O4 N N N 0 2.906 -2.602 -0.129
31 S S S1 N Y N 0 -4.341 -3.909 -1.421
32 CL CL CL1 N N N 0 -2.658 3.508 -2.297
33 CL1 CL CL2 N N N 0 -4.182 4.922 0.027
34 H15 H H1 N N N 0 3.922 -0.166 -1.965
35 H3 H H2 N N N 0 1.543 2.546 1.306
36 H4 H H3 N N N 0 1.456 1.648 -0.229
37 H6 H H4 N N N 0 2.513 0.606 2.44
38 H5 H H5 N N N 0 3.465 0.94 0.97
39 H7 H H6 N N N 0 0.739 -2.215 0.522
40 H8 H H7 N N N 0 0.714 -1.475 2.145
41 H H H8 N N N 0 -0.099 -0.151 -0.484
42 H11 H H9 N N N 0 -4.099 -1.633 0.489
43 H10 H H10 N N N 0 -3.442 -2.471 1.915
44 H13 H H11 N N N 0 -3.537 -6.988 0.234
45 H18 H H12 N N N 0 -0.723 1.748 -1.171
46 H12 H H13 N N N 0 -2.925 -4.993 1.692
47 H2 H H17 N N N 0 -1.357 2.361 3.013
48 H14 H H14 N N N 0 -4.547 -6.37 -2.011
49 H17 H H15 N N N 0 5.341 -1.398 1.731
50 H1 H H16 N N N 0 -3.135 3.983 2.503
51 H9 H H18 N N N 0 -1.459 -2.447 -0.096
52 H16 H H19 N N N 0 7.709 0.741 -1.025



LQ6 : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C17 O C doub 1.22 N N
2 N4 C17 N C sing 1.34 N N
3 N4 C19 N C sing 1.35 N N
4 O2 C19 O C doub 1.22 N N
5 C17 N3 C N sing 1.34 N N
6 C19 C18 C C sing 1.47 N N
7 N3 C16 N C sing 1.38 N N
8 C18 C16 C C doub 1.36 N N
9 C16 C15 C C sing 1.48 N N
10 O3 C15 O C doub 1.21 N N
11 C15 N1 C N sing 1.35 N N
12 N1 C7 N C sing 1.47 N N
13 N1 C6 N C sing 1.47 N N
14 C7 C8 C C sing 1.53 N N
15 C6 C5 C C sing 1.53 N N
16 C8 C9 C C sing 1.51 N N
17 C8 N C N sing 1.47 N N
18 C5 N C N sing 1.47 N N
19 O C9 O C doub 1.21 N N
20 C9 N2 C N sing 1.35 N N
21 N C4 N C sing 1.4 N N
22 N2 C10 N C sing 1.46 N N
23 C4 C20 C C doub 1.39 N Y
24 C4 C3 C C sing 1.39 N Y
25 C20 C C C sing 1.38 N Y
26 C10 C11 C C sing 1.51 N N
27 C3 C2 C C doub 1.38 N Y
28 C CL C CL sing 1.74 N N
29 C C1 C C doub 1.38 N Y
30 S C11 S C sing 1.76 N Y
31 S C14 S C sing 1.76 N Y
32 C11 C12 C C doub 1.33 N Y
33 C2 C1 C C sing 1.38 N Y
34 C1 CL1 C CL sing 1.74 N N
35 C12 C13 C C sing 1.38 N Y
36 C14 C13 C C doub 1.33 N Y
37 N3 H15 N H sing 0.97 N N
38 C5 H3 C H sing 1.09 N N
39 C5 H4 C H sing 1.09 N N
40 C6 H6 C H sing 1.09 N N
41 C6 H5 C H sing 1.09 N N
42 C7 H7 C H sing 1.09 N N
43 C7 H8 C H sing 1.09 N N
44 C8 H C H sing 1.09 N N
45 C10 H11 C H sing 1.09 N N
46 C10 H10 C H sing 1.09 N N
47 C13 H13 C H sing 1.08 N N
48 C20 H18 C H sing 1.08 N N
49 C12 H12 C H sing 1.08 N N
50 C14 H14 C H sing 1.08 N N
51 C18 H17 C H sing 1.08 N N
52 C2 H1 C H sing 1.08 N N
53 C3 H2 C H sing 1.08 N N
54 N2 H9 N H sing 0.97 N N
55 N4 H16 N H sing 0.97 N N



LQ6 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LQ6 8acd Open in New Window Bound ligand 1 1