Chemical Components in the PDB

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GKB : Summary

Code

GKB

One-letter code

X

Molecule name

(2~{R})-~{N}-[3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl]-2-(pyrimidin-5-ylamino)-2,3-dihydro-1~{H}-indene-5-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{R})-~{N}-[3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl]-2-(pyrimidin-5-ylamino)-2,3-dihydro-1~{H}-indene-5-carboxamide

Formula

C25 H21 F3 N6 O

Formal charge

0

Molecular weight

478.469 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1cn(cn1)c2cc(NC(=O)c3ccc4C[CH](Cc4c3)Nc5cncnc5)cc(c2)C(F)(F)F
SMILES OpenEye OEToolkits 2.0.6 Cc1cn(cn1)c2cc(cc(c2)NC(=O)c3ccc4c(c3)CC(C4)Nc5cncnc5)C(F)(F)F
Canonical SMILES CACTVS 3.385 Cc1cn(cn1)c2cc(NC(=O)c3ccc4C[C@H](Cc4c3)Nc5cncnc5)cc(c2)C(F)(F)F
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1cn(cn1)c2cc(cc(c2)NC(=O)c3ccc4c(c3)C[C@@H](C4)Nc5cncnc5)C(F)(F)F

IUPAC InChI

InChI=1S/C25H21F3N6O/c1-15-12-34(14-31-15)23-8-19(25(26,27)28)7-21(9-23)33-24(35)17-3-2-16-5-20(6-18(16)4-17)32-22-10-29-13-30-11-22/h2-4,7-14,20,32H,5-6H2,1H3,(H,33,35)/t20-/m1/s1

IUPAC InChI key

XFLAQLCDMJRPFH-HXUWFJFHSA-N
GKB

wwPDB Information

Atom count

56 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-09-19

Last modified at

2019-01-25

Status

Released

Obsoleted

Not Assigned



GKB : 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 Y N 0 -6.035 1.61 -0.107
2 N3 N N2 N N N 0 6.988 -0.745 0.08
3 C4 C C1 N N N 0 -4.749 -3.136 0.002
4 C5 C C2 N Y N 0 -5.367 -0.713 -0.052
5 C6 C C3 N Y N 0 -5.034 0.634 0.008
6 C7 C C4 N Y N 0 -5.856 2.969 -0.068
7 C8 C C5 N Y N 0 -7.073 3.526 -0.216
8 C10 C C6 N Y N 0 -7.363 1.388 -0.285
9 C13 C C7 N Y N 0 2.032 -0.758 -0.361
10 C15 C C8 N Y N 0 3.664 0.627 0.715
11 C17 C C9 R N N 0 5.744 -0.082 -0.32
12 C20 C C10 N Y N 0 10.558 1.153 -0.419
13 C21 C C11 N Y N 0 9.406 -0.706 0.283
14 C22 C C12 N N N 0 4.627 -1.118 -0.571
15 C24 C C13 N Y N 0 1.33 1.093 1.016
16 N N N3 N N N 0 -1.388 0.422 0.462
17 C C C14 N N N 0 -0.404 -0.323 -0.079
18 O O O1 N N N 0 -0.678 -1.267 -0.793
19 C1 C C15 N Y N 0 -2.724 0.044 0.293
20 C11 C C16 N Y N 0 -3.712 1.013 0.18
21 C12 C C17 N Y N 0 1.01 0.009 0.197
22 C14 C C18 N Y N 0 3.353 -0.449 -0.099
23 C16 C C19 N N N 0 5.167 0.752 0.843
24 C18 C C20 N Y N 0 8.212 -0.094 -0.091
25 C19 C C21 N Y N 0 8.272 1.18 -0.651
26 C2 C C22 N Y N 0 -3.063 -1.302 0.228
27 C23 C C23 N Y N 0 2.651 1.395 1.267
28 C3 C C24 N Y N 0 -4.383 -1.676 0.061
29 C9 C C25 N N N 0 -7.372 5.003 -0.23
30 F F F1 N N N 0 -3.844 -3.875 0.772
31 F1 F F2 N N N 0 -6.042 -3.314 0.506
32 F2 F F3 N N N 0 -4.701 -3.576 -1.325
33 N2 N N4 N Y N 0 -7.973 2.54 -0.343
34 N4 N N5 N Y N 0 9.451 1.764 -0.791
35 N5 N N6 N Y N 0 10.544 -0.057 0.104
36 H1 H H1 N N N 0 6.961 -1.635 0.465
37 H2 H H2 N N N 0 -6.398 -1.009 -0.182
38 H3 H H3 N N N 0 -4.919 3.491 0.058
39 H4 H H4 N N N 0 -7.835 0.42 -0.362
40 H5 H H5 N N N 0 1.79 -1.598 -0.996
41 H6 H H6 N N N 0 5.903 0.537 -1.203
42 H7 H H7 N N N 0 11.504 1.656 -0.552
43 H8 H H8 N N N 0 9.402 -1.697 0.713
44 H9 H H9 N N N 0 4.56 -1.352 -1.633
45 H10 H H10 N N N 0 4.816 -2.024 0.004
46 H11 H H11 N N N 0 0.545 1.696 1.449
47 H12 H H12 N N N 0 -1.171 1.22 0.968
48 H13 H H13 N N N 0 -3.45 2.06 0.226
49 H14 H H14 N N N 0 5.47 1.795 0.747
50 H15 H H15 N N N 0 5.5 0.348 1.799
51 H16 H H16 N N N 0 7.37 1.685 -0.962
52 H17 H H17 N N N 0 -2.295 -2.056 0.307
53 H18 H H18 N N N 0 2.898 2.234 1.901
54 H19 H H19 N N N 0 -7.57 5.344 0.786
55 H20 H H20 N N N 0 -6.516 5.544 -0.634
56 H21 H H21 N N N 0 -8.246 5.191 -0.853



GKB : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C9 C8 C C sing 1.51 N N
2 C8 N2 C N sing 1.34 N Y
3 C8 C7 C C doub 1.35 N Y
4 N2 C10 N C doub 1.3 N Y
5 C7 N1 C N sing 1.37 N Y
6 C10 N1 C N sing 1.36 N Y
7 N1 C6 N C sing 1.4 N N
8 C6 C11 C C doub 1.39 N Y
9 C6 C5 C C sing 1.39 N Y
10 C11 C1 C C sing 1.39 N Y
11 N C1 N C sing 1.4 N N
12 N C N C sing 1.35 N N
13 C5 C3 C C doub 1.38 N Y
14 C1 C2 C C doub 1.39 N Y
15 C24 C23 C C doub 1.38 N Y
16 C24 C12 C C sing 1.4 N Y
17 C23 C15 C C sing 1.39 N Y
18 C15 C16 C C sing 1.51 N N
19 C15 C14 C C doub 1.38 N Y
20 C12 C C C sing 1.48 N N
21 C12 C13 C C doub 1.39 N Y
22 C16 C17 C C sing 1.54 N N
23 C O C O doub 1.21 N N
24 C14 C13 C C sing 1.38 N Y
25 C14 C22 C C sing 1.51 N N
26 C3 C2 C C sing 1.38 N Y
27 C3 C4 C C sing 1.51 N N
28 C22 C17 C C sing 1.54 N N
29 C17 N3 C N sing 1.47 N N
30 F C4 F C sing 1.4 N N
31 C4 F2 C F sing 1.4 N N
32 C4 F1 C F sing 1.4 N N
33 N3 C18 N C sing 1.4 N N
34 C19 C18 C C doub 1.39 N Y
35 C19 N4 C N sing 1.32 N Y
36 C18 C21 C C sing 1.39 N Y
37 N4 C20 N C doub 1.32 N Y
38 C21 N5 C N doub 1.32 N Y
39 C20 N5 C N sing 1.32 N Y
40 N3 H1 N H sing 0.97 N N
41 C5 H2 C H sing 1.08 N N
42 C7 H3 C H sing 1.08 N N
43 C10 H4 C H sing 1.08 N N
44 C13 H5 C H sing 1.08 N N
45 C17 H6 C H sing 1.09 N N
46 C20 H7 C H sing 1.08 N N
47 C21 H8 C H sing 1.08 N N
48 C22 H9 C H sing 1.09 N N
49 C22 H10 C H sing 1.09 N N
50 C24 H11 C H sing 1.08 N N
51 N H12 N H sing 0.97 N N
52 C11 H13 C H sing 1.08 N N
53 C16 H14 C H sing 1.09 N N
54 C16 H15 C H sing 1.09 N N
55 C19 H16 C H sing 1.08 N N
56 C2 H17 C H sing 1.08 N N
57 C23 H18 C H sing 1.08 N N
58 C9 H19 C H sing 1.09 N N
59 C9 H20 C H sing 1.09 N N
60 C9 H21 C H sing 1.09 N N



GKB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GKB 6hp9 Open in New Window Bound ligand 2 1