Chemical Components in the PDB

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JXT : Summary

Code

JXT

One-letter code

X

Molecule name

8-bromanyl-9-pent-4-ynyl-purin-6-amine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 8-bromanyl-9-pent-4-ynyl-purin-6-amine

Formula

C10 H10 Br N5

Formal charge

0

Molecular weight

280.124 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(CCCC#C)c(Br)nc12
SMILES OpenEye OEToolkits 2.0.7 C#CCCCn1c2c(c(ncn2)N)nc1Br
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(CCCC#C)c(Br)nc12
Canonical SMILES OpenEye OEToolkits 2.0.7 C#CCCCn1c2c(c(ncn2)N)nc1Br

IUPAC InChI

InChI=1S/C10H10BrN5/c1-2-3-4-5-16-9-7(15-10(16)11)8(12)13-6-14-9/h1,6H,3-5H2,(H2,12,13,14)

IUPAC InChI key

WCMPBWUQKLZDKB-UHFFFAOYSA-N
JXT

wwPDB Information

Atom count

26 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-04-11

Last modified at

2020-02-14

Status

Released

Obsoleted

Not Assigned



JXT : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C5 C C1 N Y N 0 2.135 -0.095 0.165
2 C4 C C2 N Y N 0 1.181 -0.953 -0.407
3 C2 C C3 N Y N 0 2.738 -2.643 -0.424
4 N6 N N1 N N N 0 4.399 0.191 0.985
5 C6 C C4 N Y N 0 3.418 -0.606 0.422
6 C8 C C5 N Y N 0 0.302 1.042 -0.068
7 CAA C C6 N N N 0 -4.94 -2.704 1.386
8 CAD C C7 N N N 0 -4.273 -2.269 0.523
9 CAF C C8 N N N 0 -3.437 -1.723 -0.558
10 CAG C C9 N N N 0 -2.106 -1.238 0.022
11 CAH C C10 N N N 0 -1.237 -0.671 -1.102
12 N1 N N2 N Y N 0 3.668 -1.874 0.113
13 N3 N N3 N Y N 0 1.524 -2.207 -0.683
14 N7 N N4 N Y N 0 1.535 1.107 0.347
15 N9 N N5 N Y N 0 0.037 -0.207 -0.548
16 BR8 BR BR1 N N N 0 -0.935 2.471 -0.023
17 H1 H H1 N N N 0 2.984 -3.668 -0.66
18 H2 H H2 N N N 0 5.281 -0.173 1.158
19 H3 H H3 N N N 0 4.205 1.116 1.207
20 H4 H H4 N N N 0 -5.537 -3.093 2.157
21 H5 H H5 N N N 0 -3.249 -2.5 -1.299
22 H6 H H6 N N N 0 -3.953 -0.887 -1.03
23 H7 H H7 N N N 0 -2.294 -0.462 0.763
24 H8 H H8 N N N 0 -1.59 -2.074 0.494
25 H9 H H9 N N N 0 -1.049 -1.448 -1.844
26 H10 H H10 N N N 0 -1.753 0.164 -1.575



JXT : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N6 C6 N C sing 1.38 N N
2 C6 N1 C N doub 1.33 N Y
3 C6 C5 C C sing 1.4 N Y
4 N1 C2 N C sing 1.32 N Y
5 N7 C5 N C sing 1.36 N Y
6 N7 C8 N C doub 1.3 N Y
7 C5 C4 C C doub 1.4 N Y
8 C2 N3 C N doub 1.32 N Y
9 C8 BR8 C BR sing 1.89 N N
10 C8 N9 C N sing 1.36 N Y
11 C4 N3 C N sing 1.33 N Y
12 C4 N9 C N sing 1.37 N Y
13 CAG CAF C C sing 1.53 N N
14 CAG CAH C C sing 1.53 N N
15 N9 CAH N C sing 1.46 N N
16 CAF CAD C C sing 1.47 N N
17 CAD CAA C C trip 1.17 N N
18 C2 H1 C H sing 1.08 N N
19 N6 H2 N H sing 0.97 N N
20 N6 H3 N H sing 0.97 N N
21 CAA H4 C H sing 1.05 N N
22 CAF H5 C H sing 1.09 N N
23 CAF H6 C H sing 1.09 N N
24 CAG H7 C H sing 1.09 N N
25 CAG H8 C H sing 1.09 N N
26 CAH H9 C H sing 1.09 N N
27 CAH H10 C H sing 1.09 N N



JXT : Used in PDB Entries

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