Chemical Components in the PDB

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KHQ : Summary

Code

KHQ

One-letter code

X

Molecule name

1-[4-[(1~{R})-1-[2-[[5-[1-(cyclopropylmethyl)pyrazol-4-yl]-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]-3,3,3-tris(fluoranyl)propan-1-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 1-[4-[(1~{R})-1-[2-[[5-[1-(cyclopropylmethyl)pyrazol-4-yl]-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]-3,3,3-tris(fluoranyl)propan-1-one

Formula

C28 H31 F3 N8 O

Formal charge

0

Molecular weight

552.594 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](N1CCN(CC1)C(=O)CC(F)(F)F)c2ccnc(Nc3[nH]c4ccc(cc4n3)c5cnn(CC6CC6)c5)c2
SMILES OpenEye OEToolkits 2.0.7 CC(c1ccnc(c1)Nc2[nH]c3ccc(cc3n2)c4cnn(c4)CC5CC5)N6CCN(CC6)C(=O)CC(F)(F)F
Canonical SMILES CACTVS 3.385 C[C@@H](N1CCN(CC1)C(=O)CC(F)(F)F)c2ccnc(Nc3[nH]c4ccc(cc4n3)c5cnn(CC6CC6)c5)c2
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H](c1ccnc(c1)Nc2[nH]c3ccc(cc3n2)c4cnn(c4)CC5CC5)N6CCN(CC6)C(=O)CC(F)(F)F

IUPAC InChI

InChI=1S/C28H31F3N8O/c1-18(37-8-10-38(11-9-37)26(40)14-28(29,30)31)20-6-7-32-25(13-20)36-27-34-23-5-4-21(12-24(23)35-27)22-15-33-39(17-22)16-19-2-3-19/h4-7,12-13,15,17-19H,2-3,8-11,14,16H2,1H3,(H2,32,34,35,36)/t18-/m1/s1

IUPAC InChI key

WEFRCKPVMWDRAK-GOSISDBHSA-N
KHQ

wwPDB Information

Atom count

71 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-05-22

Last modified at

2019-12-27

Status

Released

Obsoleted

Not Assigned



KHQ : Atoms of Molecule

Total Number of Atoms: 71
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -2.407 2.013 -1.31
2 C14 C C2 N N N 0 -9.028 -3.024 0.176
3 C5 C C3 N Y N 0 -2.624 2.301 0.03
4 C6 C C4 R N N 0 -3.989 2.715 0.518
5 C11 C C5 N N N 0 -8.084 -0.766 -0.225
6 C8 C C6 N N N 0 -4.773 0.477 0.028
7 C9 C C7 N N N 0 -5.752 -0.321 -0.839
8 C13 C C8 N N N 0 -7.768 -2.24 -0.196
9 N2 N N1 N Y N 0 -0.149 1.546 -0.865
10 C3 C C9 N Y N 0 -1.145 1.635 -1.725
11 C1 C C10 N Y N 0 -0.316 1.813 0.421
12 C18 C C11 N N N 0 -7.406 1.566 -0.565
13 C19 C C12 N N N 0 -6.361 2.291 0.292
14 C20 C C13 N N N 0 -4.212 4.197 0.211
15 C21 C C14 N Y N 0 -1.56 2.199 0.908
16 C23 C C15 N Y N 0 1.974 1.221 0.838
17 C25 C C16 N Y N 0 3.567 0.466 -0.503
18 C26 C C17 N Y N 0 4.041 0.523 0.819
19 C27 C C18 N Y N 0 5.35 0.132 1.1
20 C28 C C19 N Y N 0 6.171 -0.31 0.072
21 C29 C C20 N Y N 0 5.69 -0.363 -1.239
22 C30 C C21 N Y N 0 4.398 0.022 -1.522
23 C31 C C22 N Y N 0 7.565 -0.728 0.366
24 C32 C C23 N Y N 0 8.481 -1.176 -0.541
25 C34 C C24 N N N 0 10.862 -1.955 -0.459
26 C35 C C25 N N N 0 12.017 -1.022 -0.091
27 C36 C C26 N N N 0 13.426 -1.441 -0.516
28 C37 C C27 N N N 0 12.722 -0.286 -1.233
29 C39 C C28 N Y N 0 8.185 -0.728 1.63
30 F15 F F1 N N N 0 -10.027 -2.78 -0.773
31 F16 F F2 N N N 0 -8.735 -4.391 0.203
32 F17 F F3 N N N 0 -9.475 -2.618 1.438
33 N10 N N2 N N N 0 -7.119 0.124 -0.531
34 N22 N N3 N N N 0 0.764 1.706 1.293
35 N24 N N4 N Y N 0 2.258 0.918 -0.463
36 N33 N N5 N Y N 0 9.619 -1.449 0.129
37 N38 N N6 N Y N 0 9.409 -1.161 1.483
38 N40 N N7 N Y N 0 3.022 0.989 1.589
39 N7 N N8 N N N 0 -5.016 1.914 -0.16
40 O12 O O1 N N N 0 -9.207 -0.382 0.027
41 H1 H H1 N N N 0 -3.218 2.078 -2.02
42 H2 H H2 N N N 0 -4.054 2.554 1.594
43 H3 H H3 N N N 0 -4.921 0.218 1.077
44 H4 H H4 N N N 0 -3.75 0.24 -0.264
45 H5 H H5 N N N 0 -5.537 -0.143 -1.893
46 H6 H H6 N N N 0 -5.652 -1.384 -0.62
47 H7 H H7 N N N 0 -6.99 -2.43 0.544
48 H8 H H8 N N N 0 -7.42 -2.556 -1.179
49 H9 H H9 N N N 0 -0.972 1.41 -2.767
50 H10 H H10 N N N 0 -8.402 1.751 -0.163
51 H11 H H11 N N N 0 -7.351 1.926 -1.593
52 H12 H H12 N N N 0 -6.491 3.368 0.189
53 H13 H H13 N N N 0 -6.487 2.007 1.336
54 H14 H H14 N N N 0 -3.45 4.792 0.714
55 H15 H H15 N N N 0 -4.147 4.359 -0.865
56 H16 H H16 N N N 0 -5.199 4.497 0.564
57 H17 H H17 N N N 0 -1.693 2.416 1.958
58 H18 H H18 N N N 0 5.723 0.173 2.113
59 H19 H H19 N N N 0 6.335 -0.707 -2.034
60 H20 H H20 N N N 0 4.032 -0.021 -2.537
61 H21 H H21 N N N 0 8.322 -1.291 -1.603
62 H22 H H22 N N N 0 10.76 -1.997 -1.544
63 H23 H H23 N N N 0 11.065 -2.954 -0.074
64 H24 H H24 N N N 0 11.913 -0.496 0.858
65 H25 H H25 N N N 0 14.249 -1.191 0.153
66 H26 H H26 N N N 0 13.53 -2.381 -1.058
67 H27 H H27 N N N 0 12.362 -0.467 -2.246
68 H28 H H28 N N N 0 13.082 0.723 -1.035
69 H29 H H29 N N N 0 7.728 -0.423 2.56
70 H30 H H30 N N N 0 0.666 1.972 2.221
71 H31 H H31 N N N 0 1.655 1.003 -1.218



KHQ : Chemical Bonds

Total Number of Bonds: 76
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 C6 C C sing 1.53 N N
2 C18 C19 C C sing 1.53 N N
3 C18 N10 C N sing 1.47 N N
4 C19 N7 C N sing 1.47 N N
5 F17 C14 F C sing 1.4 N N
6 C13 C14 C C sing 1.53 N N
7 C13 C11 C C sing 1.51 N N
8 N7 C6 N C sing 1.47 N N
9 N7 C8 N C sing 1.47 N N
10 C6 C5 C C sing 1.51 N N
11 C14 F15 C F sing 1.4 N N
12 C14 F16 C F sing 1.4 N N
13 C4 C5 C C doub 1.39 N Y
14 C4 C3 C C sing 1.38 N Y
15 N10 C11 N C sing 1.35 N N
16 N10 C9 N C sing 1.47 N N
17 C11 O12 C O doub 1.21 N N
18 C5 C21 C C sing 1.38 N Y
19 C3 N2 C N doub 1.32 N Y
20 C9 C8 C C sing 1.53 N N
21 C21 C1 C C doub 1.39 N Y
22 N2 C1 N C sing 1.32 N Y
23 C1 N22 C N sing 1.39 N N
24 N22 C23 N C sing 1.38 N N
25 N40 C23 N C doub 1.31 N Y
26 N40 C26 N C sing 1.36 N Y
27 C23 N24 C N sing 1.37 N Y
28 C36 C37 C C sing 1.53 N N
29 C36 C35 C C sing 1.53 N N
30 C26 C27 C C doub 1.39 N Y
31 C26 C25 C C sing 1.41 N Y
32 C37 C35 C C sing 1.53 N N
33 N24 C25 N C sing 1.39 N Y
34 C27 C28 C C sing 1.39 N Y
35 C25 C30 C C doub 1.39 N Y
36 C35 C34 C C sing 1.53 N N
37 C32 C31 C C doub 1.36 N Y
38 C32 N33 C N sing 1.35 N Y
39 C28 C31 C C sing 1.48 N N
40 C28 C29 C C doub 1.4 N Y
41 C34 N33 C N sing 1.47 N N
42 C30 C29 C C sing 1.38 N Y
43 C31 C39 C C sing 1.41 N Y
44 N33 N38 N N sing 1.4 N Y
45 C39 N38 C N doub 1.31 N Y
46 C4 H1 C H sing 1.08 N N
47 C6 H2 C H sing 1.09 N N
48 C8 H3 C H sing 1.09 N N
49 C8 H4 C H sing 1.09 N N
50 C9 H5 C H sing 1.09 N N
51 C9 H6 C H sing 1.09 N N
52 C13 H7 C H sing 1.09 N N
53 C13 H8 C H sing 1.09 N N
54 C3 H9 C H sing 1.08 N N
55 C18 H10 C H sing 1.09 N N
56 C18 H11 C H sing 1.09 N N
57 C19 H12 C H sing 1.09 N N
58 C19 H13 C H sing 1.09 N N
59 C20 H14 C H sing 1.09 N N
60 C20 H15 C H sing 1.09 N N
61 C20 H16 C H sing 1.09 N N
62 C21 H17 C H sing 1.08 N N
63 C27 H18 C H sing 1.08 N N
64 C29 H19 C H sing 1.08 N N
65 C30 H20 C H sing 1.08 N N
66 C32 H21 C H sing 1.08 N N
67 C34 H22 C H sing 1.09 N N
68 C34 H23 C H sing 1.09 N N
69 C35 H24 C H sing 1.09 N N
70 C36 H25 C H sing 1.09 N N
71 C36 H26 C H sing 1.09 N N
72 C37 H27 C H sing 1.09 N N
73 C37 H28 C H sing 1.09 N N
74 C39 H29 C H sing 1.08 N N
75 N22 H30 N H sing 0.97 N N
76 N24 H31 N H sing 0.97 N N



KHQ : Used in PDB Entries

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