Chemical Components in the PDB

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EX0 : Summary

Code

EX0

One-letter code

X

Molecule name

2-ethoxy-8-(5-fluoranylpyridin-3-yl)-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purin-6-amine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-9-[[4-[[(1~{S},4~{S})-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purin-6-amine

Formula

C26 H29 F N8 O

Formal charge

0

Molecular weight

488.56 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCOc1nc(N)c2nc(n(Cc3ccc(CN4C[CH]5C[CH]4CN5C)cc3)c2n1)c6cncc(F)c6
SMILES OpenEye OEToolkits 2.0.7 CCOc1nc(c2c(n1)n(c(n2)c3cc(cnc3)F)Cc4ccc(cc4)CN5CC6CC5CN6C)N
Canonical SMILES CACTVS 3.385 CCOc1nc(N)c2nc(n(Cc3ccc(CN4C[C@@H]5C[C@H]4CN5C)cc3)c2n1)c6cncc(F)c6
Canonical SMILES OpenEye OEToolkits 2.0.7 CCOc1nc(c2c(n1)n(c(n2)c3cc(cnc3)F)Cc4ccc(cc4)CN5C[C@@H]6C[C@H]5CN6C)N

IUPAC InChI

InChI=1S/C26H29FN8O/c1-3-36-26-31-23(28)22-25(32-26)35(24(30-22)18-8-19(27)11-29-10-18)13-17-6-4-16(5-7-17)12-34-15-20-9-21(34)14-33(20)2/h4-8,10-11,20-21H,3,9,12-15H2,1-2H3,(H2,28,31,32)/t20-,21-/m0/s1

IUPAC InChI key

NHZSWKDFGUWVJJ-SFTDATJTSA-N
EX0

wwPDB Information

Atom count

65 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-02-13

Last modified at

2020-11-06

Status

Released

Obsoleted

Not Assigned



EX0 : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N Y N 0 3.872 -0.86 0.693
2 C C C1 N Y N 0 3.314 0.739 -0.949
3 O O O1 N N N 0 5.594 -2.347 0.327
4 C12 C C5 N Y N 0 0.089 -1.474 1.857
5 C1 C C2 N Y N 0 3.101 0.153 0.312
6 C10 C C3 N Y N 0 -2.249 -0.001 1.912
7 C11 C C4 N Y N 0 -2.3 -1.371 1.734
8 C13 C C6 N Y N 0 -1.13 -2.107 1.706
9 C14 C C7 N Y N 0 0.559 2.762 0.199
10 C15 C C8 N Y N 0 -0.228 3.193 -0.874
11 C16 C C9 N Y N 0 0.286 3.253 1.476
12 C17 C C10 N Y N 0 -1.251 4.092 -0.618
13 C18 C C11 N Y N 0 -1.458 4.532 0.679
14 C19 C C12 N N N 0 -3.629 -2.061 1.571
15 C2 C C13 N Y N 0 4.343 0.222 -1.757
16 C20 C C14 N N N 0 -4.314 -0.758 -0.366
17 C21 C C15 S N N 0 -5.206 -2.945 -0.075
18 C22 C C16 S N N 0 -5.797 -0.855 -0.842
19 C23 C C17 N N N 0 -5.32 -3.051 -1.627
20 C24 C C18 N N N 0 -4.764 -1.148 -3.038
21 C25 C C19 N N N 0 -6.341 -1.895 0.202
22 C3 C C20 N Y N 0 4.829 -1.313 -0.099
23 C4 C C21 N Y N 0 1.66 1.798 -0.016
24 C5 C C22 N N N 0 6.616 -2.806 -0.561
25 C6 C C23 N N N 0 7.37 -3.969 0.087
26 C7 C C24 N N N 0 1.469 0.586 2.199
27 C8 C C25 N Y N 0 0.14 -0.104 2.035
28 C9 C C26 N Y N 0 -1.03 0.632 2.063
29 F F F1 N N N 0 -2.037 4.536 -1.623
30 N1 N N2 N Y N 0 5.065 -0.792 -1.294
31 N2 N N3 N Y N 0 2.408 1.733 -1.09
32 N3 N N4 N Y N 0 2.055 0.836 0.88
33 N7 N N8 N N N 0 -5.73 -1.699 -2.077
34 N4 N N5 N N N 0 4.597 0.759 -3.006
35 N5 N N6 N Y N 0 -0.697 4.107 1.67
36 N6 N N7 N N N 0 -3.984 -2.11 0.146
37 H1 H H1 N N N 0 -3.163 0.576 1.929
38 H2 H H2 N N N 0 1.003 -2.05 1.836
39 H3 H H3 N N N 0 -1.17 -3.178 1.568
40 H4 H H4 N N N 0 -0.044 2.833 -1.876
41 H5 H H5 N N N 0 0.886 2.928 2.314
42 H6 H H6 N N N 0 -2.253 5.233 0.883
43 H7 H H7 N N N 0 -3.563 -3.076 1.963
44 H8 H H8 N N N 0 -4.395 -1.509 2.117
45 H9 H H9 N N N 0 -3.665 -0.5 -1.203
46 H10 H H10 N N N 0 -4.22 -0.018 0.429
47 H11 H H11 N N N 0 -5.266 -3.883 0.478
48 H12 H H12 N N N 0 -6.341 0.086 -0.919
49 H13 H H13 N N N 0 -4.356 -3.318 -2.06
50 H14 H H14 N N N 0 -6.076 -3.786 -1.902
51 H15 H H15 N N N 0 -3.754 -1.265 -2.645
52 H16 H H16 N N N 0 -4.85 -1.682 -3.984
53 H17 H H17 N N N 0 -4.972 -0.09 -3.197
54 H18 H H18 N N N 0 -7.328 -2.272 -0.064
55 H19 H H19 N N N 0 -6.312 -1.512 1.222
56 H20 H H20 N N N 0 6.163 -3.141 -1.494
57 H21 H H21 N N N 0 7.311 -1.992 -0.766
58 H22 H H22 N N N 0 7.822 -3.634 1.02
59 H23 H H23 N N N 0 6.674 -4.783 0.292
60 H24 H H24 N N N 0 8.149 -4.319 -0.59
61 H25 H H25 N N N 0 1.325 1.533 2.718
62 H26 H H26 N N N 0 2.139 -0.049 2.78
63 H27 H H27 N N N 0 -0.99 1.703 2.202
64 H28 H H28 N N N 0 4.063 1.5 -3.334
65 H29 H H29 N N N 0 5.31 0.395 -3.555



EX0 : Chemical Bonds

Total Number of Bonds: 70
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N C1 N C doub 1.33 N Y
2 N C3 N C sing 1.32 N Y
3 C C1 C C sing 1.41 N Y
4 C C2 C C doub 1.41 N Y
5 C N2 C N sing 1.35 N Y
6 O C3 O C sing 1.35 N N
7 O C5 O C sing 1.43 N N
8 C1 N3 C N sing 1.37 N Y
9 C10 C11 C C doub 1.38 N Y
10 C10 C9 C C sing 1.38 N Y
11 C11 C13 C C sing 1.38 N Y
12 C11 C19 C C sing 1.51 N N
13 C12 C13 C C doub 1.38 N Y
14 C12 C8 C C sing 1.38 N Y
15 C14 C15 C C doub 1.4 N Y
16 C14 C16 C C sing 1.4 N Y
17 C14 C4 C C sing 1.48 N N
18 C15 C17 C C sing 1.39 N Y
19 C16 N5 C N doub 1.32 N Y
20 C17 C18 C C doub 1.39 N Y
21 C17 F C F sing 1.35 N N
22 C18 N5 C N sing 1.32 N Y
23 C19 N6 C N sing 1.47 N N
24 C2 N1 C N sing 1.33 N Y
25 C2 N4 C N sing 1.38 N N
26 C20 C22 C C sing 1.56 N N
27 C20 N6 C N sing 1.48 N N
28 C21 C23 C C sing 1.56 N N
29 C21 C25 C C sing 1.57 N N
30 C21 N6 C N sing 1.5 N N
31 C22 C25 C C sing 1.57 N N
32 C22 N7 C N sing 1.5 N N
33 C23 N7 C N sing 1.48 N N
34 C24 N7 C N sing 1.47 N N
35 C3 N1 C N doub 1.32 N Y
36 C4 N2 C N doub 1.31 N Y
37 C4 N3 C N sing 1.37 N Y
38 C5 C6 C C sing 1.53 N N
39 C7 C8 C C sing 1.51 N N
40 C7 N3 C N sing 1.46 N N
41 C8 C9 C C doub 1.38 N Y
42 C10 H1 C H sing 1.08 N N
43 C12 H2 C H sing 1.08 N N
44 C13 H3 C H sing 1.08 N N
45 C15 H4 C H sing 1.08 N N
46 C16 H5 C H sing 1.08 N N
47 C18 H6 C H sing 1.08 N N
48 C19 H7 C H sing 1.09 N N
49 C19 H8 C H sing 1.09 N N
50 C20 H9 C H sing 1.09 N N
51 C20 H10 C H sing 1.09 N N
52 C21 H11 C H sing 1.09 N N
53 C22 H12 C H sing 1.09 N N
54 C23 H13 C H sing 1.09 N N
55 C23 H14 C H sing 1.09 N N
56 C24 H15 C H sing 1.09 N N
57 C24 H16 C H sing 1.09 N N
58 C24 H17 C H sing 1.09 N N
59 C25 H18 C H sing 1.09 N N
60 C25 H19 C H sing 1.09 N N
61 C5 H20 C H sing 1.09 N N
62 C5 H21 C H sing 1.09 N N
63 C6 H22 C H sing 1.09 N N
64 C6 H23 C H sing 1.09 N N
65 C6 H24 C H sing 1.09 N N
66 C7 H25 C H sing 1.09 N N
67 C7 H26 C H sing 1.09 N N
68 C9 H27 C H sing 1.08 N N
69 N4 H28 N H sing 0.97 N N
70 N4 H29 N H sing 0.97 N N



EX0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EX0 6lw0 Open in New Window Bound ligand 2 1