Chemical Components in the PDB

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EX4 : Summary

Code

EX4

One-letter code

X

Molecule name

(5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one
OpenEye OEToolkits 2.0.6 (5~{R})-4-[4-[4-[4-fluoranyl-3-(trifluoromethyl)phenyl]-1-(2-pyrrolidin-1-ylethyl)imidazol-2-yl]piperidin-1-yl]-5-methyl-6,8-dihydro-5~{H}-pyrido[2,3-d]pyrimidin-7-one

Formula

C29 H33 F4 N7 O

Formal charge

0

Molecular weight

571.612 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c2c(c1ccc(F)c(c1)C(F)(F)F)nc(n2CCN3CCCC3)C4CCN(CC4)c6ncnc5NC(=O)CC(C)c56
SMILES CACTVS 3.385 C[CH]1CC(=O)Nc2ncnc(N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(F)c(c6)C(F)(F)F)c12
SMILES OpenEye OEToolkits 2.0.6 CC1CC(=O)Nc2c1c(ncn2)N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(c(c6)C(F)(F)F)F
Canonical SMILES CACTVS 3.385 C[C@@H]1CC(=O)Nc2ncnc(N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(F)c(c6)C(F)(F)F)c12
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@@H]1CC(=O)Nc2c1c(ncn2)N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(c(c6)C(F)(F)F)F

IUPAC InChI

InChI=1S/C29H33F4N7O/c1-18-14-24(41)37-26-25(18)28(35-17-34-26)39-10-6-19(7-11-39)27-36-23(16-40(27)13-12-38-8-2-3-9-38)20-4-5-22(30)21(15-20)29(31,32)33/h4-5,15-19H,2-3,6-14H2,1H3,(H,34,35,37,41)/t18-/m1/s1

IUPAC InChI key

XIYKGCYSJCRNDN-GOSISDBHSA-N
EX4

wwPDB Information

Atom count

74 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-02-08

Last modified at

2018-04-27

Status

Released

Obsoleted

Not Assigned



EX4 : Atoms of Molecule

Total Number of Atoms: 74
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C7 C C1 N Y N 0 -3.148 -1.754 -0.613
2 C6 C C2 N Y N 0 -2.987 -0.426 -0.377
3 C1 C C3 N N N 0 2.607 -0.649 -1.593
4 N1 N N1 N Y N 0 -1.663 -0.176 -0.32
5 C5 C C4 N Y N 0 -1.009 -1.288 -0.511
6 C4 C C5 N N N 0 0.491 -1.43 -0.522
7 C3 C C6 N N N 0 1.057 -0.988 0.83
8 C2 C C7 N N N 0 2.585 -1.077 0.792
9 O O O1 N N N 0 7.209 4.318 0.879
10 C28 C C8 N N N 0 6.608 3.271 0.767
11 N6 N N2 N N N 0 7.237 2.192 0.269
12 C23 C C9 N Y N 0 6.539 1.021 0.009
13 N5 N N3 N Y N 0 7.186 -0.119 -0.22
14 C22 C C10 N Y N 0 6.521 -1.233 -0.454
15 N4 N N4 N Y N 0 5.204 -1.272 -0.473
16 C27 C C11 N N N 0 5.165 3.192 1.193
17 C25 C C12 R N N 0 4.387 2.3 0.225
18 C26 C C13 N N N 0 4.197 3.034 -1.104
19 C24 C C14 N Y N 0 5.152 1.024 -0.013
20 C21 C C15 N Y N 0 4.485 -0.17 -0.258
21 N N N5 N N N 0 3.1 -0.215 -0.279
22 C C C16 N N N 0 1.081 -0.548 -1.626
23 N2 N N6 N Y N 0 -1.894 -2.293 -0.691
24 C8 C C17 N N N 0 -1.569 -3.701 -0.935
25 C9 C C18 N N N 0 -1.341 -4.41 0.401
26 N3 N N7 N N N 0 -1.015 -5.822 0.157
27 C13 C C19 N N N 0 -0.558 -6.481 1.394
28 C12 C C20 N N N 0 -1.483 -7.692 1.636
29 C11 C C21 N N N 0 -2.054 -7.983 0.224
30 C10 C C22 N N N 0 -2.191 -6.555 -0.359
31 C14 C C23 N Y N 0 -4.073 0.572 -0.211
32 C19 C C24 N Y N 0 -5.403 0.159 -0.19
33 C18 C C25 N Y N 0 -6.41 1.09 -0.035
34 C17 C C26 N Y N 0 -6.1 2.433 0.099
35 F F F1 N N N 0 -7.089 3.341 0.25
36 C16 C C27 N Y N 0 -4.778 2.848 0.08
37 C15 C C28 N Y N 0 -3.765 1.924 -0.07
38 C20 C C29 N N N 0 -4.446 4.311 0.226
39 F1 F F2 N N N 0 -4.93 4.778 1.453
40 F2 F F3 N N N 0 -3.059 4.482 0.176
41 F3 F F4 N N N 0 -5.043 5.031 -0.815
42 H1 H H1 N N N 0 -4.084 -2.282 -0.715
43 H2 H H2 N N N 0 3.031 -0.011 -2.369
44 H3 H H3 N N N 0 2.907 -1.683 -1.77
45 H4 H H4 N N N 0 0.757 -2.471 -0.706
46 H5 H H5 N N N 0 0.757 0.04 1.032
47 H6 H H6 N N N 0 0.674 -1.64 1.616
48 H7 H H7 N N N 0 2.991 -0.749 1.749
49 H8 H H8 N N N 0 2.884 -2.108 0.604
50 H9 H H9 N N N 0 8.189 2.233 0.087
51 H10 H H10 N N N 0 7.073 -2.143 -0.637
52 H11 H H11 N N N 0 5.107 2.775 2.199
53 H12 H H12 N N N 0 4.731 4.192 1.19
54 H13 H H13 N N N 0 3.412 2.065 0.652
55 H17 H H17 N N N 0 0.781 0.487 -1.463
56 H14 H H14 N N N 0 5.172 3.27 -1.531
57 H15 H H15 N N N 0 3.643 2.399 -1.794
58 H16 H H16 N N N 0 3.642 3.957 -0.933
59 H18 H H18 N N N 0 0.714 -0.885 -2.596
60 H19 H H19 N N N 0 -2.395 -4.178 -1.463
61 H20 H H20 N N N 0 -0.665 -3.766 -1.54
62 H21 H H21 N N N 0 -0.515 -3.933 0.93
63 H22 H H22 N N N 0 -2.245 -4.346 1.007
64 H24 H H24 N N N 0 0.472 -6.818 1.275
65 H25 H H25 N N N 0 -0.628 -5.787 2.232
66 H26 H H26 N N N 0 -0.913 -8.544 2.005
67 H27 H H27 N N N 0 -2.283 -7.433 2.33
68 H28 H H28 N N N 0 -1.356 -8.58 -0.364
69 H29 H H29 N N N 0 -3.025 -8.474 0.289
70 H30 H H30 N N N 0 -3.112 -6.089 -0.01
71 H31 H H31 N N N 0 -2.17 -6.586 -1.449
72 H32 H H32 N N N 0 -5.646 -0.888 -0.295
73 H33 H H33 N N N 0 -7.442 0.771 -0.019
74 H34 H H34 N N N 0 -2.735 2.248 -0.085



EX4 : Chemical Bonds

Total Number of Bonds: 79
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 N5 C N sing 1.32 N Y
2 C22 N4 C N doub 1.32 N Y
3 N5 C23 N C doub 1.33 N Y
4 N4 C21 N C sing 1.33 N Y
5 C23 N6 C N sing 1.39 N N
6 C23 C24 C C sing 1.39 N Y
7 C26 C25 C C sing 1.53 N N
8 F3 C20 F C sing 1.4 N N
9 C21 C24 C C doub 1.39 N Y
10 C21 N C N sing 1.39 N N
11 C1 C C C sing 1.53 N N
12 C1 N C N sing 1.47 N N
13 N6 C28 N C sing 1.34 N N
14 C24 C25 C C sing 1.51 N N
15 C C4 C C sing 1.53 N N
16 N C2 N C sing 1.47 N N
17 F1 C20 F C sing 1.4 N N
18 C25 C27 C C sing 1.53 N N
19 C20 C16 C C sing 1.51 N N
20 C20 F2 C F sing 1.4 N N
21 C28 O C O doub 1.21 N N
22 C28 C27 C C sing 1.51 N N
23 C15 C16 C C doub 1.38 N Y
24 C15 C14 C C sing 1.39 N Y
25 C16 C17 C C sing 1.39 N Y
26 C4 C5 C C sing 1.51 N N
27 C4 C3 C C sing 1.53 N N
28 C5 N1 C N doub 1.3 N Y
29 C5 N2 C N sing 1.35 N Y
30 C2 C3 C C sing 1.53 N N
31 N1 C6 N C sing 1.35 N Y
32 N2 C7 N C sing 1.37 N Y
33 N2 C8 N C sing 1.47 N N
34 C6 C7 C C doub 1.36 N Y
35 C6 C14 C C sing 1.48 N N
36 C14 C19 C C doub 1.39 N Y
37 C8 C9 C C sing 1.53 N N
38 C17 F C F sing 1.35 N N
39 C17 C18 C C doub 1.38 N Y
40 C19 C18 C C sing 1.38 N Y
41 C9 N3 C N sing 1.47 N N
42 N3 C13 N C sing 1.47 N N
43 N3 C10 N C sing 1.48 N N
44 C13 C12 C C sing 1.54 N N
45 C10 C11 C C sing 1.55 N N
46 C12 C11 C C sing 1.55 N N
47 C7 H1 C H sing 1.08 N N
48 C1 H2 C H sing 1.09 N N
49 C1 H3 C H sing 1.09 N N
50 C4 H4 C H sing 1.09 N N
51 C3 H5 C H sing 1.09 N N
52 C3 H6 C H sing 1.09 N N
53 C2 H7 C H sing 1.09 N N
54 C2 H8 C H sing 1.09 N N
55 N6 H9 N H sing 0.97 N N
56 C22 H10 C H sing 1.08 N N
57 C27 H11 C H sing 1.09 N N
58 C27 H12 C H sing 1.09 N N
59 C25 H13 C H sing 1.09 N N
60 C26 H14 C H sing 1.09 N N
61 C26 H15 C H sing 1.09 N N
62 C26 H16 C H sing 1.09 N N
63 C H17 C H sing 1.09 N N
64 C H18 C H sing 1.09 N N
65 C8 H19 C H sing 1.09 N N
66 C8 H20 C H sing 1.09 N N
67 C9 H21 C H sing 1.09 N N
68 C9 H22 C H sing 1.09 N N
69 C13 H24 C H sing 1.09 N N
70 C13 H25 C H sing 1.09 N N
71 C12 H26 C H sing 1.09 N N
72 C12 H27 C H sing 1.09 N N
73 C11 H28 C H sing 1.09 N N
74 C11 H29 C H sing 1.09 N N
75 C10 H30 C H sing 1.09 N N
76 C10 H31 C H sing 1.09 N N
77 C19 H32 C H sing 1.08 N N
78 C18 H33 C H sing 1.08 N N
79 C15 H34 C H sing 1.08 N N



EX4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EX4 6ccy Open in New Window Bound ligand 1 1