Chemical Components in the PDB

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FN9 : Summary

Code

FN9

One-letter code

X

Molecule name

3,5-dimethyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]pyrrolo[3,2-d]pyrimidin-4-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 3,5-dimethyl-2-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyrrolo[3,2-d]pyrimidin-4-one

Formula

C20 H25 N5 O

Formal charge

0

Molecular weight

351.445 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1C[CH](C[CH](C1)c2ccccc2)NC3=Nc4ccn(C)c4C(=O)N3C
SMILES OpenEye OEToolkits 2.0.7 Cn1ccc2c1C(=O)N(C(=N2)NC3CC(CN(C3)C)c4ccccc4)C
Canonical SMILES CACTVS 3.385 CN1C[C@@H](C[C@@H](C1)c2ccccc2)NC3=Nc4ccn(C)c4C(=O)N3C
Canonical SMILES OpenEye OEToolkits 2.0.7 Cn1ccc2c1C(=O)N(C(=N2)N[C@@H]3C[C@@H](CN(C3)C)c4ccccc4)C

IUPAC InChI

InChI=1S/C20H25N5O/c1-23-12-15(14-7-5-4-6-8-14)11-16(13-23)21-20-22-17-9-10-24(2)18(17)19(26)25(20)3/h4-10,15-16H,11-13H2,1-3H3,(H,21,22)/t15-,16+/m0/s1

IUPAC InChI key

FAOILJOQEQTGLJ-JKSUJKDBSA-N
FN9

wwPDB Information

Atom count

51 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-06-08

Last modified at

2021-04-02

Status

Released

Obsoleted

Not Assigned



FN9 : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C13 C C1 N Y N 0 -5.244 1.648 -1.262
2 C15 C C2 N N N 0 -6.772 -0.214 -0.541
3 C17 C C3 N N N 0 -3.872 -1.303 0.321
4 C20 C C4 N N N 0 -2.13 -2.75 1.221
5 C21 C C5 N Y N 0 4.464 -0.114 -0.512
6 C22 C C6 N Y N 0 4.994 -0.819 0.553
7 C24 C C7 N Y N 0 6.928 -1.345 -0.756
8 C26 C C8 N Y N 0 5.167 -0.025 -1.699
9 C01 C C9 N N N 0 1.893 3.307 1.873
10 C03 C C10 N N N 0 3.166 1.582 0.749
11 C04 C C11 R N N 0 3.119 0.551 -0.381
12 C05 C C12 N N N 0 2.056 -0.503 -0.06
13 C06 C C13 R N N 0 0.703 0.188 0.131
14 C07 C C14 N N N 0 0.821 1.229 1.247
15 C09 C C15 N N N 0 -1.634 -0.569 0.226
16 C11 C C16 N Y N 0 -3.264 0.829 -0.638
17 C12 C C17 N Y N 0 -3.924 1.921 -1.241
18 C16 C C18 N Y N 0 -4.255 -0.102 -0.303
19 C23 C C19 N Y N 0 6.225 -1.434 0.431
20 C25 C C20 N Y N 0 6.399 -0.64 -1.821
21 N02 N N1 N N N 0 1.849 2.216 0.891
22 N08 N N2 N N N 0 -0.308 -0.807 0.494
23 N10 N N3 N N N 0 -1.975 0.556 -0.357
24 N14 N N4 N Y N 0 -5.465 0.429 -0.699
25 N19 N N5 N N N 0 -2.56 -1.509 0.572
26 O18 O O1 N N N 0 -4.704 -2.14 0.628
27 H131 H H1 N N N 0 -6.009 2.299 -1.66
28 H151 H H2 N N N 0 -6.989 -0.818 -1.422
29 H153 H H3 N N N 0 -6.757 -0.853 0.342
30 H152 H H4 N N N 0 -7.541 0.549 -0.425
31 H201 H H5 N N N 0 -2.999 -3.376 1.421
32 H203 H H6 N N N 0 -1.442 -3.284 0.564
33 H202 H H7 N N N 0 -1.627 -2.515 2.159
34 H221 H H8 N N N 0 4.445 -0.888 1.481
35 H241 H H9 N N N 0 7.89 -1.826 -0.852
36 H261 H H10 N N N 0 4.753 0.525 -2.531
37 H013 H H11 N N N 0 2.193 2.911 2.844
38 H012 H H12 N N N 0 2.614 4.058 1.549
39 H011 H H13 N N N 0 0.906 3.762 1.955
40 H032 H H14 N N N 0 3.432 1.085 1.682
41 H031 H H15 N N N 0 3.912 2.342 0.517
42 H041 H H16 N N N 0 2.866 1.049 -1.317
43 H051 H H17 N N N 0 1.988 -1.215 -0.883
44 H052 H H18 N N N 0 2.329 -1.029 0.855
45 H061 H H19 N N N 0 0.412 0.681 -0.797
46 H071 H H20 N N N 0 -0.137 1.734 1.375
47 H072 H H21 N N N 0 1.098 0.734 2.177
48 H121 H H22 N N N 0 -3.454 2.817 -1.62
49 H231 H H23 N N N 0 6.639 -1.984 1.263
50 H251 H H24 N N N 0 6.948 -0.571 -2.749
51 H081 H H26 N N N 0 -0.042 -1.635 0.924



FN9 : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C15 N14 C N sing 1.47 N N
2 C13 N14 C N sing 1.36 N Y
3 C13 C12 C C doub 1.35 N Y
4 N14 C16 N C sing 1.38 N Y
5 C12 C11 C C sing 1.41 N Y
6 C16 C11 C C doub 1.4 N Y
7 C16 C17 C C sing 1.41 N N
8 O18 C17 O C doub 1.22 N N
9 C11 N10 C N sing 1.35 N N
10 C17 N19 C N sing 1.35 N N
11 N10 C09 N C doub 1.31 N N
12 N19 C09 N C sing 1.36 N N
13 N19 C20 N C sing 1.46 N N
14 C09 N08 C N sing 1.37 N N
15 C07 C06 C C sing 1.53 N N
16 C07 N02 C N sing 1.47 N N
17 N08 C06 N C sing 1.46 N N
18 C01 N02 C N sing 1.47 N N
19 C06 C05 C C sing 1.53 N N
20 N02 C03 N C sing 1.47 N N
21 C05 C04 C C sing 1.53 N N
22 C03 C04 C C sing 1.53 N N
23 C04 C21 C C sing 1.51 N N
24 C21 C26 C C doub 1.38 N Y
25 C21 C22 C C sing 1.38 N Y
26 C26 C25 C C sing 1.38 N Y
27 C22 C23 C C doub 1.38 N Y
28 C25 C24 C C doub 1.38 N Y
29 C23 C24 C C sing 1.38 N Y
30 C13 H131 C H sing 1.08 N N
31 C15 H151 C H sing 1.09 N N
32 C15 H153 C H sing 1.09 N N
33 C15 H152 C H sing 1.09 N N
34 C20 H201 C H sing 1.09 N N
35 C20 H203 C H sing 1.09 N N
36 C20 H202 C H sing 1.09 N N
37 C22 H221 C H sing 1.08 N N
38 C24 H241 C H sing 1.08 N N
39 C26 H261 C H sing 1.08 N N
40 C01 H013 C H sing 1.09 N N
41 C01 H012 C H sing 1.09 N N
42 C01 H011 C H sing 1.09 N N
43 C03 H032 C H sing 1.09 N N
44 C03 H031 C H sing 1.09 N N
45 C04 H041 C H sing 1.09 N N
46 C05 H051 C H sing 1.09 N N
47 C05 H052 C H sing 1.09 N N
48 C06 H061 C H sing 1.09 N N
49 C07 H071 C H sing 1.09 N N
50 C07 H072 C H sing 1.09 N N
51 C12 H121 C H sing 1.08 N N
52 C23 H231 C H sing 1.08 N N
53 C25 H251 C H sing 1.08 N N
54 N08 H081 N H sing 0.97 N N



FN9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
FN9 7c9n Open in New Window Bound ligand 2 1