Chemical Components in the PDB

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JYQ : Summary

Code

JYQ

One-letter code

X

Molecule name

~{S}-[4-(6-aminopurin-9-yl)butyl] ethanethioate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{S}-[4-(6-aminopurin-9-yl)butyl] ethanethioate

Formula

C11 H15 N5 O S

Formal charge

0

Molecular weight

265.335 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(=O)SCCCCn1cnc2c(N)ncnc12
SMILES OpenEye OEToolkits 2.0.7 CC(=O)SCCCCn1cnc2c1ncnc2N
Canonical SMILES CACTVS 3.385 CC(=O)SCCCCn1cnc2c(N)ncnc12
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(=O)SCCCCn1cnc2c1ncnc2N

IUPAC InChI

InChI=1S/C11H15N5OS/c1-8(17)18-5-3-2-4-16-7-15-9-10(12)13-6-14-11(9)16/h6-7H,2-5H2,1H3,(H2,12,13,14)

IUPAC InChI key

MLUWWHOQAYWORL-UHFFFAOYSA-N
JYQ

wwPDB Information

Atom count

33 (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



JYQ : Atoms of Molecule

Total Number of Atoms: 33
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 3.737 0.353 0.334
2 C8 C C2 N Y N 0 2.378 2.042 0.368
3 C2 C C3 N Y N 0 3.555 -2.056 -0.835
4 N3 N N1 N Y N 0 2.556 -1.211 -0.974
5 N6 N N2 N N N 0 5.916 -0.288 1.185
6 N7 N N3 N Y N 0 3.534 1.615 0.784
7 C4 C C4 N Y N 0 2.605 -0.006 -0.416
8 C6 C C5 N Y N 0 4.777 -0.585 0.458
9 CAA C C6 N N N 0 -7.134 -0.645 0.35
10 CAF C C7 N N N 0 -1.984 0.686 -0.769
11 CAG C C8 N N N 0 -0.612 0.578 -0.1
12 CAH C C9 N N N 0 -3.048 0.083 0.149
13 CAI C C10 N N N 0 0.453 1.182 -1.018
14 CAN C C11 N N N 0 -5.647 -0.516 0.561
15 N1 N N4 N Y N 0 4.639 -1.764 -0.139
16 N9 N N5 N Y N 0 1.766 1.079 -0.377
17 OAC O O1 N N N 0 -5.142 -0.928 1.585
18 SAM S S1 N N N 0 -4.671 0.21 -0.643
19 H1 H H1 N N N 0 1.964 3.017 0.581
20 H2 H H2 N N N 0 3.483 -3.028 -1.301
21 H3 H H3 N N N 0 6.626 -0.944 1.263
22 H4 H H4 N N N 0 6.004 0.576 1.617
23 H5 H H5 N N N 0 -7.4 -0.223 -0.619
24 H6 H H6 N N N 0 -7.415 -1.698 0.377
25 H7 H H7 N N N 0 -7.661 -0.107 1.138
26 H8 H H8 N N N 0 -2.216 1.735 -0.955
27 H9 H H9 N N N 0 -1.97 0.144 -1.715
28 H10 H H10 N N N 0 -0.626 1.12 0.846
29 H11 H H11 N N N 0 -0.38 -0.47 0.086
30 H12 H H12 N N N 0 -2.816 -0.966 0.335
31 H13 H H13 N N N 0 -3.062 0.624 1.095
32 H14 H H14 N N N 0 0.466 0.64 -1.964
33 H15 H H15 N N N 0 0.22 2.231 -1.204



JYQ : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAC CAN O C doub 1.21 N N
2 CAN SAM C S sing 1.71 N N
3 CAN CAA C C sing 1.51 N N
4 SAM CAH S C sing 1.81 N N
5 N6 C6 N C sing 1.38 N N
6 CAH CAF C C sing 1.53 N N
7 C6 N1 C N doub 1.33 N Y
8 C6 C5 C C sing 1.41 N Y
9 CAF CAG C C sing 1.53 N N
10 N1 C2 N C sing 1.32 N Y
11 N7 C5 N C sing 1.36 N Y
12 N7 C8 N C doub 1.3 N Y
13 C5 C4 C C doub 1.4 N Y
14 C2 N3 C N doub 1.32 N Y
15 C8 N9 C N sing 1.36 N Y
16 C4 N3 C N sing 1.33 N Y
17 C4 N9 C N sing 1.37 N Y
18 N9 CAI N C sing 1.46 N N
19 CAG CAI C C sing 1.53 N N
20 C8 H1 C H sing 1.08 N N
21 C2 H2 C H sing 1.08 N N
22 N6 H3 N H sing 0.97 N N
23 N6 H4 N H sing 0.97 N N
24 CAA H5 C H sing 1.09 N N
25 CAA H6 C H sing 1.09 N N
26 CAA H7 C H sing 1.09 N N
27 CAF H8 C H sing 1.09 N N
28 CAF H9 C H sing 1.09 N N
29 CAG H10 C H sing 1.09 N N
30 CAG H11 C H sing 1.09 N N
31 CAH H12 C H sing 1.09 N N
32 CAH H13 C H sing 1.09 N N
33 CAI H14 C H sing 1.09 N N
34 CAI H15 C H sing 1.09 N N



JYQ : Used in PDB Entries

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