Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

XDE : Summary

Code

XDE

One-letter code

X

Molecule name

4-[(1S)-1-hydroxy-2-(methylamino)ethyl]benzene-1,2-diol

Systematic names

ProgramVersionName
ACDLabs 12.01 4-[(1S)-1-hydroxy-2-(methylamino)ethyl]benzene-1,2-diol
OpenEye OEToolkits 1.7.6 4-[(1S)-2-(methylamino)-1-oxidanyl-ethyl]benzene-1,2-diol

Formula

C9 H13 N O3

Formal charge

0

Molecular weight

183.204 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Oc1ccc(cc1O)C(O)CNC
SMILES CACTVS 3.370 CNC[CH](O)c1ccc(O)c(O)c1
SMILES OpenEye OEToolkits 1.7.6 CNCC(c1ccc(c(c1)O)O)O
Canonical SMILES CACTVS 3.370 CNC[C@@H](O)c1ccc(O)c(O)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 CNC[C@H](c1ccc(c(c1)O)O)O

IUPAC InChI

InChI=1S/C9H13NO3/c1-10-5-9(13)6-2-3-7(11)8(12)4-6/h2-4,9-13H,5H2,1H3/t9-/m1/s1

IUPAC InChI key

UCTWMZQNUQWSLP-SECBINFHSA-N
XDE

wwPDB Information

Atom count

26 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-03-13

Last modified at

2013-03-15

Status

Released

Obsoleted

Not Assigned



XDE : 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 C1 C C1 N Y N 0 -0.057 -0.158 0.359
2 C2 C C2 N Y N 0 0.796 0.914 0.541
3 C3 C C3 N Y N 0 2.126 0.813 0.167
4 C4 C C4 N Y N 0 2.601 -0.37 -0.393
5 C5 C C5 N Y N 0 1.74 -1.441 -0.572
6 C6 C C6 N Y N 0 0.414 -1.334 -0.196
7 O1 O O1 N N N 0 2.967 1.867 0.344
8 O2 O O2 N N N 0 3.905 -0.474 -0.762
9 O3 O O3 N N N 0 -1.918 -1.274 1.378
10 C9 C C9 N N N 0 -4.615 0.73 -1.2
11 N1 N N1 N N N 0 -3.755 0.457 -0.041
12 C8 C C8 N N N 0 -2.365 0.231 -0.458
13 C7 C C7 S N N 0 -1.502 -0.049 0.773
14 H1 H H1 N N N 0 0.426 1.831 0.975
15 H2 H H2 N N N 0 2.105 -2.36 -1.006
16 H3 H H3 N N N 0 -0.255 -2.169 -0.336
17 H4 H H4 N N N 0 3.414 1.874 1.202
18 H5 H H5 N N N 0 4.487 -0.803 -0.064
19 H6 H H6 N N N 0 -1.845 -2.044 0.798
20 H7 H H7 N N N 0 -4.589 -0.121 -1.881
21 H8 H H8 N N N 0 -5.639 0.893 -0.863
22 H9 H H9 N N N 0 -4.257 1.62 -1.717
23 H10 H H10 N N N 0 -4.104 -0.325 0.492
24 H12 H H12 N N N 0 -2.323 -0.623 -1.134
25 H13 H H13 N N N 0 -1.991 1.118 -0.97
26 H14 H H14 N N N 0 -1.614 0.766 1.488



XDE : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C7 O C sing 1.43 N N
2 C7 C8 C C sing 1.53 N N
3 C7 C1 C C sing 1.51 N N
4 C2 C1 C C doub 1.38 N Y
5 C2 C3 C C sing 1.39 N Y
6 O1 C3 O C sing 1.36 N N
7 C8 N1 C N sing 1.47 N N
8 C1 C6 C C sing 1.38 N Y
9 C3 C4 C C doub 1.39 N Y
10 N1 C9 N C sing 1.47 N N
11 C6 C5 C C doub 1.38 N Y
12 C4 C5 C C sing 1.39 N Y
13 C4 O2 C O sing 1.36 N N
14 C2 H1 C H sing 1.08 N N
15 C5 H2 C H sing 1.08 N N
16 C6 H3 C H sing 1.08 N N
17 O1 H4 O H sing 0.97 N N
18 O2 H5 O H sing 0.97 N N
19 O3 H6 O H sing 0.97 N N
20 C9 H7 C H sing 1.09 N N
21 C9 H8 C H sing 1.09 N N
22 C9 H9 C H sing 1.09 N N
23 N1 H10 N H sing 1.01 N N
24 C8 H12 C H sing 1.09 N N
25 C8 H13 C H sing 1.09 N N
26 C7 H14 C H sing 1.09 N N



XDE : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XDE 3pah Open in New Window Bound ligand 1 1