Chemical Components in the PDB

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JXB : Summary

Code

JXB

One-letter code

X

Molecule name

9-(4-azidobutyl)-8-bromanyl-purin-6-amine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 9-(4-azidobutyl)-8-bromanyl-purin-6-amine

Formula

C9 H11 Br N8

Formal charge

0

Molecular weight

311.141 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(CCCCN=[N+]=[N-])c(Br)nc12
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(c(n2)Br)CCCCN=[N+]=[N-])N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(CCCCN=[N+]=[N-])c(Br)nc12
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(c(n2)Br)CCCCN=[N+]=[N-])N

IUPAC InChI

InChI=1S/C9H11BrN8/c10-9-16-6-7(11)13-5-14-8(6)18(9)4-2-1-3-15-17-12/h5H,1-4H2,(H2,11,13,14)

IUPAC InChI key

UOIUSKVGBLVETF-UHFFFAOYSA-N
JXB

wwPDB Information

Atom count

29 (18 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



JXB : Atoms of Molecule

Total Number of Atoms: 29
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N -1 7.005 -0.27 0.679
2 C C C1 N N N 0 3.944 -1.324 0.56
3 C1 C C2 N N N 0 2.972 -0.958 -0.562
4 C2 C C3 N N N 0 1.577 -0.732 0.025
5 C3 C C4 N N N 0 0.604 -0.366 -1.097
6 C4 C C5 N Y N 0 -1.234 1.034 -0.08
7 C5 C C6 N Y N 0 -2.804 -0.437 0.203
8 C6 C C7 N Y N 0 -3.96 -1.184 0.484
9 C7 C C8 N Y N 0 -2.904 -3.063 -0.343
10 C8 C C9 N Y N 0 -1.707 -1.101 -0.37
11 N1 N N2 N N N 1 6.142 -0.905 0.339
12 N2 N N3 N N N 0 5.28 -1.54 -0.002
13 N3 N N4 N Y N 0 -0.731 -0.149 -0.535
14 N4 N N5 N Y N 0 -2.449 0.863 0.355
15 N5 N N6 N N N 0 -5.072 -0.584 1.047
16 N6 N N7 N Y N 0 -3.96 -2.482 0.195
17 N7 N N8 N Y N 0 -1.8 -2.403 -0.623
18 BR BR BR1 N N N 0 -0.301 2.679 -0.075
19 H2 H H2 N N N 0 3.983 -0.513 1.287
20 H3 H H3 N N N 0 3.605 -2.236 1.052
21 H4 H H4 N N N 0 3.311 -0.046 -1.054
22 H5 H H5 N N N 0 2.933 -1.769 -1.289
23 H6 H H6 N N N 0 1.238 -1.644 0.516
24 H7 H H7 N N N 0 1.616 0.079 0.752
25 H8 H H8 N N N 0 0.943 0.547 -1.589
26 H9 H H9 N N N 0 0.565 -1.177 -1.824
27 H10 H H10 N N N 0 -2.946 -4.12 -0.561
28 H11 H H11 N N N 0 -5.865 -1.111 1.236
29 H12 H H12 N N N 0 -5.06 0.364 1.253



JXB : Chemical Bonds

Total Number of Bonds: 30
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N N1 N N doub 1.12 N N
2 N1 N2 N N doub 1.12 N N
3 N2 C N C sing 1.47 N N
4 C C1 C C sing 1.53 N N
5 N5 C6 N C sing 1.38 N N
6 C1 C2 C C sing 1.53 N N
7 C6 N6 C N doub 1.33 N Y
8 C6 C5 C C sing 1.4 N Y
9 N6 C7 N C sing 1.32 N Y
10 N4 C5 N C sing 1.36 N Y
11 N4 C4 N C doub 1.3 N Y
12 C5 C8 C C doub 1.4 N Y
13 C7 N7 C N doub 1.32 N Y
14 C2 C3 C C sing 1.53 N N
15 C4 BR C BR sing 1.89 N N
16 C4 N3 C N sing 1.36 N Y
17 C8 N7 C N sing 1.33 N Y
18 C8 N3 C N sing 1.37 N Y
19 N3 C3 N C sing 1.46 N N
20 C H2 C H sing 1.09 N N
21 C H3 C H sing 1.09 N N
22 C1 H4 C H sing 1.09 N N
23 C1 H5 C H sing 1.09 N N
24 C2 H6 C H sing 1.09 N N
25 C2 H7 C H sing 1.09 N N
26 C3 H8 C H sing 1.09 N N
27 C3 H9 C H sing 1.09 N N
28 C7 H10 C H sing 1.08 N N
29 N5 H11 N H sing 0.97 N N
30 N5 H12 N H sing 0.97 N N



JXB : Used in PDB Entries

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