Chemical Components in the PDB

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HLJ : Summary

Code

HLJ

One-letter code

X

Molecule name

N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide
OpenEye OEToolkits 2.0.6 3-[(2-azanylidene-3-methyl-imidazol-1-yl)methyl]-~{N}-[(3,4-dichlorophenyl)methyl]-5-(6-fluoranyl-2-methyl-pyridin-3-yl)benzamide

Formula

C25 H22 Cl2 F N5 O

Formal charge

0

Molecular weight

498.379 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N(Cc1cc(c(cc1)Cl)Cl)C(=O)c4cc(c2c(C)nc(cc2)F)cc(CN3\C(=N)N(C)C=C3)c4
SMILES CACTVS 3.385 CN1C=CN(Cc2cc(cc(c2)c3ccc(F)nc3C)C(=O)NCc4ccc(Cl)c(Cl)c4)C1=N
SMILES OpenEye OEToolkits 2.0.6 Cc1c(ccc(n1)F)c2cc(cc(c2)C(=O)NCc3ccc(c(c3)Cl)Cl)CN4C=CN(C4=N)C
Canonical SMILES CACTVS 3.385 CN1C=CN(Cc2cc(cc(c2)c3ccc(F)nc3C)C(=O)NCc4ccc(Cl)c(Cl)c4)C1=N
Canonical SMILES OpenEye OEToolkits 2.0.6 [H]/N=C/1\N(C=CN1Cc2cc(cc(c2)C(=O)NCc3ccc(c(c3)Cl)Cl)c4ccc(nc4C)F)C

IUPAC InChI

InChI=1S/C25H22Cl2FN5O/c1-15-20(4-6-23(28)31-15)18-9-17(14-33-8-7-32(2)25(33)29)10-19(12-18)24(34)30-13-16-3-5-21(26)22(27)11-16/h3-12,29H,13-14H2,1-2H3,(H,30,34)/b29-25+

IUPAC InChI key

ZPVQIJIWGMKMQN-XLVZBRSZSA-N
HLJ

wwPDB Information

Atom count

56 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-07-11

Last modified at

2019-03-08

Status

Released

Obsoleted

Not Assigned



HLJ : Atoms of Molecule

Total Number of Atoms: 56
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 -1.202 -1.68 -0.307
2 N3 N N2 N N N 0 5.554 -1.042 -0.399
3 C4 C C1 N Y N 0 -4.422 -1.602 -0.737
4 C5 C C2 N Y N 0 -5.619 -1.043 -0.329
5 C6 C C3 N Y N 0 -5.931 -0.984 1.019
6 C7 C C4 N Y N 0 -5.045 -1.485 1.956
7 C8 C C5 N Y N 0 -3.849 -2.043 1.546
8 C10 C C6 N Y N 0 0.783 0.364 -0.417
9 C13 C C7 N Y N 0 0.347 3.38 -0.703
10 C15 C C8 N Y N 0 0.782 5.324 0.458
11 C17 C C9 N Y N 0 2.239 3.457 0.778
12 C20 C C10 N N N 0 4.777 -0.675 -1.586
13 C21 C C11 N N N 0 5.672 -2.299 0.132
14 C22 C C12 N N N 0 6.878 -3.309 2.11
15 C24 C C13 N N N 0 6.306 -0.177 0.386
16 C1 C C14 N N N 0 0.053 -2.001 -0.679
17 C11 C C15 N Y N 0 1.771 1.341 -0.474
18 C12 C C16 N Y N 0 1.446 2.747 -0.129
19 C14 C C17 N N N 0 -0.519 2.629 -1.682
20 C16 C C18 N Y N 0 1.895 4.766 1.067
21 C18 C C19 N Y N 0 3.068 0.997 -0.854
22 C19 C C20 N Y N 0 3.374 -0.311 -1.175
23 C2 C C21 N N N 0 -2.235 -2.717 -0.245
24 C23 C C22 N N N 0 6.862 -0.875 1.367
25 C25 C C23 N Y N 0 2.398 -1.287 -1.121
26 C3 C C24 N Y N 0 -3.537 -2.102 0.201
27 C9 C C25 N Y N 0 1.096 -0.955 -0.742
28 F1 F F1 N N N 0 0.441 6.601 0.737
29 N2 N N3 N Y N 0 0.053 4.627 -0.394
30 N4 N N4 N N N 0 6.482 -2.205 1.232
31 N5 N N5 N N N 0 5.112 -3.391 -0.328
32 O1 O O1 N N N 0 0.328 -3.151 -0.962
33 CL1 CL CL1 N N N 0 -6.73 -0.414 -1.506
34 CL2 CL CL2 N N N 0 -7.433 -0.282 1.533
35 H1 H H1 N N N 0 -1.42 -0.763 -0.077
36 H2 H H2 N N N 0 -4.18 -1.652 -1.788
37 H3 H H3 N N N 0 -5.288 -1.439 3.007
38 H4 H H4 N N N 0 -3.157 -2.434 2.277
39 H5 H H5 N N N 0 -0.221 0.625 -0.118
40 H6 H H6 N N N 0 3.099 2.996 1.241
41 H7 H H7 N N N 0 5.245 0.178 -2.076
42 H11 H H11 N N N 0 7.414 -4.06 1.53
43 H8 H H8 N N N 0 4.747 -1.519 -2.275
44 H9 H H9 N N N 0 7.527 -2.93 2.9
45 H10 H H10 N N N 0 5.989 -3.757 2.553
46 H12 H H12 N N N 0 6.42 0.885 0.225
47 H13 H H13 N N N 0 -1.32 2.122 -1.144
48 H14 H H14 N N N 0 -0.95 3.33 -2.398
49 H15 H H15 N N N 0 0.086 1.894 -2.212
50 H16 H H16 N N N 0 2.485 5.344 1.763
51 H17 H H17 N N N 0 3.836 1.756 -0.899
52 H18 H H18 N N N 0 -2.363 -3.162 -1.231
53 H19 H H19 N N N 0 -1.935 -3.487 0.466
54 H20 H H20 N N N 0 7.503 -0.477 2.14
55 H21 H H21 N N N 0 2.643 -2.308 -1.374
56 H22 H H22 N N N 0 4.551 -3.352 -1.118



HLJ : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 N4 C N sing 1.47 N N
2 C23 N4 C N sing 1.39 N N
3 C23 C24 C C doub 1.33 N N
4 N4 C21 N C sing 1.37 N N
5 C24 N3 C N sing 1.39 N N
6 C21 N3 C N sing 1.37 N N
7 C21 N5 C N doub 1.31 N N
8 N3 C20 N C sing 1.47 N N
9 C20 C19 C C sing 1.51 N N
10 C18 C19 C C doub 1.38 N Y
11 C18 C11 C C sing 1.39 N Y
12 F1 C15 F C sing 1.35 N N
13 C19 C25 C C sing 1.38 N Y
14 C15 C16 C C doub 1.39 N Y
15 C15 N2 C N sing 1.32 N Y
16 C16 C17 C C sing 1.38 N Y
17 N2 C13 N C doub 1.32 N Y
18 C13 C14 C C sing 1.51 N N
19 C13 C12 C C sing 1.39 N Y
20 C17 C12 C C doub 1.4 N Y
21 C12 C11 C C sing 1.48 N N
22 C11 C10 C C doub 1.39 N Y
23 C25 C9 C C doub 1.4 N Y
24 C10 C9 C C sing 1.39 N Y
25 C9 C1 C C sing 1.48 N N
26 C1 O1 C O doub 1.22 N N
27 C1 N1 C N sing 1.35 N N
28 CL1 C5 CL C sing 1.74 N N
29 N1 C2 N C sing 1.47 N N
30 C5 C4 C C doub 1.38 N Y
31 C5 C6 C C sing 1.38 N Y
32 C4 C3 C C sing 1.38 N Y
33 CL2 C6 CL C sing 1.74 N N
34 C6 C7 C C doub 1.38 N Y
35 C3 C2 C C sing 1.51 N N
36 C3 C8 C C doub 1.38 N Y
37 C7 C8 C C sing 1.38 N Y
38 N1 H1 N H sing 0.97 N N
39 C4 H2 C H sing 1.08 N N
40 C7 H3 C H sing 1.08 N N
41 C8 H4 C H sing 1.08 N N
42 C10 H5 C H sing 1.08 N N
43 C17 H6 C H sing 1.08 N N
44 C20 H7 C H sing 1.09 N N
45 C20 H8 C H sing 1.09 N N
46 C22 H9 C H sing 1.09 N N
47 C22 H10 C H sing 1.09 N N
48 C22 H11 C H sing 1.09 N N
49 C24 H12 C H sing 1.08 N N
50 C14 H13 C H sing 1.09 N N
51 C14 H14 C H sing 1.09 N N
52 C14 H15 C H sing 1.09 N N
53 C16 H16 C H sing 1.08 N N
54 C18 H17 C H sing 1.08 N N
55 C2 H18 C H sing 1.09 N N
56 C2 H19 C H sing 1.09 N N
57 C23 H20 C H sing 1.08 N N
58 C25 H21 C H sing 1.08 N N
59 N5 H22 N H sing 0.97 N N



HLJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
HLJ 6e23 Open in New Window Bound ligand 2 1