Chemical Components in the PDB

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S6C : Summary

Code

S6C

One-letter code

X

Molecule name

[(3S)-1-(7H-purin-6-yl)piperidin-3-yl]acetic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 [(3S)-1-(7H-purin-6-yl)piperidin-3-yl]acetic acid
OpenEye OEToolkits 2.0.7 2-[(3~{S})-1-(7~{H}-purin-6-yl)piperidin-3-yl]ethanoic acid

Formula

C12 H15 N5 O2

Formal charge

0

Molecular weight

261.28 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CC1CCCN(C1)c1ncnc2nc[NH]c12
SMILES CACTVS 3.385 OC(=O)C[CH]1CCCN(C1)c2ncnc3nc[nH]c23
SMILES OpenEye OEToolkits 2.0.7 c1[nH]c2c(n1)ncnc2N3CCCC(C3)CC(=O)O
Canonical SMILES CACTVS 3.385 OC(=O)C[C@@H]1CCCN(C1)c2ncnc3nc[nH]c23
Canonical SMILES OpenEye OEToolkits 2.0.7 c1[nH]c2c(n1)ncnc2N3CCC[C@H](C3)CC(=O)O

IUPAC InChI

InChI=1S/C12H15N5O2/c18-9(19)4-8-2-1-3-17(5-8)12-10-11(14-6-13-10)15-7-16-12/h6-8H,1-5H2,(H,18,19)(H,13,14,15,16)/t8-/m0/s1

IUPAC InChI key

OHVACHOAZRWEJX-QMMMGPOBSA-N
S6C

wwPDB Information

Atom count

34 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-06-23

Last modified at

2022-07-08

Status

Released

Obsoleted

Not Assigned



S6C : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C18 C C1 N N N 0 -0.86 1.373 -0.313
2 C16 C C2 N Y N 0 2.923 2.186 0.304
3 C14 C C3 N Y N 0 3.64 -0.002 0.352
4 C12 C C4 N Y N 0 3.639 -2.169 0.282
5 C10 C C5 N Y N 0 2.319 -0.419 0.117
6 C02 C C6 N N N 0 -4.17 -0.185 0.813
7 C03 C C7 N N N 0 -2.699 0.142 0.848
8 C04 C C8 S N N 0 -2.323 0.933 -0.407
9 C05 C C9 N N N 0 -2.507 0.049 -1.643
10 C06 C C10 N N N 0 -1.561 -1.152 -1.548
11 C07 C C11 N N N 0 -0.121 -0.652 -1.421
12 C09 C C12 N Y N 0 1.323 0.551 -0.007
13 N08 N N1 N N N 0 0.004 0.188 -0.223
14 N11 N N2 N Y N 0 2.355 -1.797 0.079
15 N13 N N3 N Y N 0 4.391 -1.116 0.442
16 N15 N N4 N Y N 0 3.892 1.308 0.438
17 N17 N N5 N Y N 0 1.669 1.832 0.088
18 O01 O O1 N N N 0 -4.847 0.177 -0.12
19 H181 H H1 N N N 0 -0.596 1.948 -1.201
20 O19 O O2 N N N 0 -4.727 -0.879 1.817
21 H182 H H2 N N N 0 -0.722 1.991 0.574
22 H161 H H3 N N N 0 3.161 3.237 0.378
23 H121 H H4 N N N 0 3.991 -3.19 0.307
24 H031 H H5 N N N 0 -2.481 0.739 1.733
25 H032 H H6 N N N 0 -2.122 -0.782 0.881
26 H041 H H7 N N N 0 -2.962 1.812 -0.488
27 H052 H H8 N N N 0 -3.538 -0.302 -1.69
28 H051 H H9 N N N 0 -2.277 0.624 -2.54
29 H062 H H10 N N N 0 -1.818 -1.748 -0.672
30 H061 H H11 N N N 0 -1.657 -1.763 -2.445
31 H072 H H12 N N N 0 0.554 -1.504 -1.339
32 H071 H H13 N N N 0 0.14 -0.067 -2.304
33 H111 H H14 N N N 0 1.6 -2.388 -0.068
34 H2 H H16 N N N 0 -5.674 -1.065 1.751



S6C : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C06 C05 C C sing 1.53 N N
2 C06 C07 C C sing 1.53 N N
3 C05 C04 C C sing 1.53 N N
4 C07 N08 C N sing 1.47 N N
5 C04 C03 C C sing 1.53 N N
6 C04 C18 C C sing 1.53 N N
7 C03 C02 C C sing 1.51 N N
8 N08 C18 N C sing 1.47 N N
9 N08 C09 N C sing 1.38 N N
10 N17 C09 N C doub 1.33 N Y
11 N17 C16 N C sing 1.32 N Y
12 C09 C10 C C sing 1.4 N Y
13 C02 O01 C O doub 1.21 N N
14 C02 O19 C O sing 1.34 N N
15 C16 N15 C N doub 1.31 N Y
16 C10 N11 C N sing 1.38 N Y
17 C10 C14 C C doub 1.41 N Y
18 N15 C14 N C sing 1.34 N Y
19 N11 C12 N C sing 1.35 N Y
20 C14 N13 C N sing 1.35 N Y
21 C12 N13 C N doub 1.3 N Y
22 C18 H181 C H sing 1.09 N N
23 C18 H182 C H sing 1.09 N N
24 C16 H161 C H sing 1.08 N N
25 C12 H121 C H sing 1.08 N N
26 C03 H031 C H sing 1.09 N N
27 C03 H032 C H sing 1.09 N N
28 C04 H041 C H sing 1.09 N N
29 C05 H052 C H sing 1.09 N N
30 C05 H051 C H sing 1.09 N N
31 C06 H062 C H sing 1.09 N N
32 C06 H061 C H sing 1.09 N N
33 C07 H072 C H sing 1.09 N N
34 C07 H071 C H sing 1.09 N N
35 N11 H111 N H sing 0.97 N N
36 O19 H2 O H sing 0.97 N N



S6C : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
S6C 5spr Open in New Window Bound ligand 1 1