Chemical Components in the PDB

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JDL : Summary

Code

JDL

One-letter code

X

Molecule name

6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-imine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-imine

Formula

C11 H12 F N3

Formal charge

0

Molecular weight

205.231 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1Cc2cc(F)cc3CCN(C1=N)c23
SMILES OpenEye OEToolkits 2.0.7 CN1Cc2cc(cc3c2N(C1=N)CC3)F
Canonical SMILES CACTVS 3.385 CN1Cc2cc(F)cc3CCN(C1=N)c23
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C\1/N(Cc2cc(cc3c2N1CC3)F)C

IUPAC InChI

InChI=1S/C11H12FN3/c1-14-6-8-5-9(12)4-7-2-3-15(10(7)8)11(14)13/h4-5,13H,2-3,6H2,1H3/b13-11-

IUPAC InChI key

FHPIUPDPCMWKJY-QBFSEMIESA-N
JDL

wwPDB Information

Atom count

27 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-21

Last modified at

2022-05-13

Status

Released

Obsoleted

Not Assigned



JDL : Atoms of Molecule

Total Number of Atoms: 27
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C9 C C1 N Y N 0 -2.462 0.85 -0.15
2 C12 C C2 N Y N 0 -1.708 -1.422 0.191
3 C6 C C3 N Y N 0 -1.155 1.298 -0.114
4 C13 C C4 N Y N 0 -0.41 -0.983 0.226
5 C5 C C5 N Y N 0 -0.15 0.38 0.067
6 C10 C C6 N Y N 0 -2.733 -0.502 0.003
7 C3 C C7 N N N 0 2.233 0.134 0.193
8 C7 C C8 N N N 0 -0.514 2.661 -0.238
9 C14 C C9 N N N 0 0.788 -1.87 0.45
10 C8 C C10 N N N 0 1.004 2.397 -0.118
11 C1 C C11 N N N 0 2.939 -1.968 -0.902
12 N4 N N1 N N N 0 1.132 0.962 0.054
13 H1 H H1 N N N 0 -3.271 1.552 -0.292
14 N2 N N2 N N N 0 1.992 -1.209 -0.082
15 N15 N N3 N N N 0 3.405 0.579 0.553
16 F11 F F1 N N N 0 -4.013 -0.931 -0.032
17 H2 H H2 N N N 0 -1.933 -2.472 0.308
18 H4 H H4 N N N 0 -0.747 3.103 -1.207
19 H5 H H5 N N N 0 0.913 -2.049 1.518
20 H6 H H6 N N N 0 0.638 -2.82 -0.063
21 H7 H H7 N N N 0 1.515 2.715 -1.026
22 H8 H H8 N N N 0 3.761 -1.319 -1.203
23 H9 H H9 N N N 0 3.331 -2.806 -0.325
24 H10 H H10 N N N 0 2.431 -2.345 -1.79
25 H12 H H12 N N N 0 3.53 1.523 0.735
26 H3 H H3 N N N 0 -0.852 3.314 0.567
27 H15 H H15 N N N 0 1.411 2.92 0.747



JDL : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N2 C N sing 1.46 N N
2 N2 C3 N C sing 1.39 N N
3 N2 C14 N C sing 1.47 N N
4 N15 C3 N C doub 1.3 N N
5 C3 N4 C N sing 1.38 N N
6 C14 C13 C C sing 1.51 N N
7 N4 C5 N C sing 1.41 N N
8 N4 C8 N C sing 1.45 N N
9 C13 C5 C C doub 1.4 N Y
10 C13 C12 C C sing 1.37 N Y
11 C5 C6 C C sing 1.37 N Y
12 C8 C7 C C sing 1.55 N N
13 C12 C10 C C doub 1.39 N Y
14 C6 C7 C C sing 1.51 N N
15 C6 C9 C C doub 1.38 N Y
16 C10 C9 C C sing 1.39 N Y
17 C10 F11 C F sing 1.35 N N
18 C9 H1 C H sing 1.08 N N
19 C12 H2 C H sing 1.08 N N
20 C7 H4 C H sing 1.09 N N
21 C14 H5 C H sing 1.09 N N
22 C14 H6 C H sing 1.09 N N
23 C8 H7 C H sing 1.09 N N
24 C1 H8 C H sing 1.09 N N
25 C1 H9 C H sing 1.09 N N
26 C1 H10 C H sing 1.09 N N
27 N15 H12 N H sing 0.97 N N
28 C7 H3 C H sing 1.09 N N
29 C8 H15 C H sing 1.09 N N



JDL : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JDL 7eu5 Open in New Window Bound ligand 4 1