Chemical Components in the PDB

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W2J : Summary

Code

W2J

One-letter code

X

Molecule name

[(3R,5R)-5-methylpiperidin-3-yl]methanol

Systematic names

ProgramVersionName
ACDLabs 12.01 [(3R,5R)-5-methylpiperidin-3-yl]methanol
OpenEye OEToolkits 2.0.7 [(3~{R},5~{R})-5-methylpiperidin-3-yl]methanol

Formula

C7 H15 N O

Formal charge

0

Molecular weight

129.2 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(CC(CO)CNC1)C
SMILES CACTVS 3.385 C[CH]1CNC[CH](CO)C1
SMILES OpenEye OEToolkits 2.0.7 CC1CC(CNC1)CO
Canonical SMILES CACTVS 3.385 C[C@H]1CNC[C@H](CO)C1
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H]1C[C@H](CNC1)CO

IUPAC InChI

InChI=1S/C7H15NO/c1-6-2-7(5-9)4-8-3-6/h6-9H,2-5H2,1H3/t6-,7-/m1/s1

IUPAC InChI key

SSKKCWRWVKPDIA-RNFRBKRXSA-N
W2J

wwPDB Information

Atom count

24 (9 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-24

Last modified at

2021-01-08

Status

Released

Obsoleted

Not Assigned



W2J : Atoms of Molecule

Total Number of Atoms: 24
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 R N N 0 1.718 -0.711 0.352
2 C5 C C2 N N N 0 1.929 -1.121 -1.107
3 C6 C C3 N N N 0 0.29 -1.06 0.781
4 O O O1 N N N 0 -3.055 0.089 -0.483
5 C C C4 N N N 0 -2.128 -0.562 0.388
6 C1 C C5 R N N 0 -0.7 -0.264 -0.074
7 C3 C C6 N N N 0 1.934 0.797 0.496
8 N N N1 N N N 0 0.964 1.514 -0.341
9 C2 C C7 N N N 0 -0.413 1.231 0.082
10 H1 H H1 N N N 0 2.428 -1.243 0.986
11 H2 H H2 N N N 0 1.219 -0.589 -1.74
12 H3 H H3 N N N 0 2.945 -0.873 -1.411
13 H4 H H4 N N N 0 1.771 -2.195 -1.209
14 H5 H H5 N N N 0 0.118 -2.127 0.639
15 H6 H H6 N N N 0 0.153 -0.806 1.832
16 H7 H H7 N N N 0 -3.982 -0.056 -0.249
17 H8 H H8 N N N 0 -2.265 -0.194 1.405
18 H9 H H9 N N N 0 -2.3 -1.638 0.364
19 H10 H H10 N N N 0 -0.589 -0.549 -1.12
20 H11 H H11 N N N 0 1.798 1.086 1.538
21 H12 H H12 N N N 0 2.946 1.051 0.178
22 H13 H H13 N N N 0 1.147 2.506 -0.338
23 H15 H H15 N N N 0 -1.107 1.8 -0.536
24 H16 H H16 N N N 0 -0.539 1.518 1.126



W2J : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3 N C N sing 1.47 N N
2 C3 C4 C C sing 1.53 N N
3 O C O C sing 1.43 N N
4 N C2 N C sing 1.47 N N
5 C2 C1 C C sing 1.53 N N
6 C1 C C C sing 1.53 N N
7 C1 C6 C C sing 1.53 N N
8 C5 C4 C C sing 1.53 N N
9 C4 C6 C C sing 1.53 N N
10 C4 H1 C H sing 1.09 N N
11 C5 H2 C H sing 1.09 N N
12 C5 H3 C H sing 1.09 N N
13 C5 H4 C H sing 1.09 N N
14 C6 H5 C H sing 1.09 N N
15 C6 H6 C H sing 1.09 N N
16 O H7 O H sing 0.97 N N
17 C H8 C H sing 1.09 N N
18 C H9 C H sing 1.09 N N
19 C1 H10 C H sing 1.09 N N
20 C3 H11 C H sing 1.09 N N
21 C3 H12 C H sing 1.09 N N
22 N H13 N H sing 1.01 N N
23 C2 H15 C H sing 1.09 N N
24 C2 H16 C H sing 1.09 N N



W2J : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
W2J 5s3u Open in New Window Bound ligand 1 1