Chemical Components in the PDB

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SRO : Summary

Code

SRO

One-letter code

X

Molecule name

SEROTONIN

Synonyms

3-(2-AMINOETHYL)-1H-INDOL-5-OL

Systematic names

ProgramVersionName
ACDLabs 10.04 3-(2-aminoethyl)-1H-indol-5-ol
OpenEye OEToolkits 1.5.0 3-(2-aminoethyl)-1H-indol-5-ol

Formula

C10 H12 N2 O

Formal charge

0

Molecular weight

176.215 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Oc1cc2c(cc1)ncc2CCN
SMILES CACTVS 3.341 NCCc1c[nH]c2ccc(O)cc12
SMILES OpenEye OEToolkits 1.5.0 c1cc2c(cc1O)c(c[nH]2)CCN
Canonical SMILES CACTVS 3.341 NCCc1c[nH]c2ccc(O)cc12
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc2c(cc1O)c(c[nH]2)CCN

IUPAC InChI

InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2

IUPAC InChI key

QZAYGJVTTNCVMB-UHFFFAOYSA-N
SRO

wwPDB Information

Atom count

25 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-07-11

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



SRO : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OH O OH N N N 0 -2.747 2.407 -0.069
2 CZ3 C CZ3 N Y N 0 -2.163 1.18 -0.014
3 CH2 C CH2 N Y N 0 -2.936 0.056 0.269
4 CZ2 C CZ2 N Y N 0 -2.361 -1.193 0.329
5 CE2 C CE2 N Y N 0 -0.996 -1.342 0.104
6 NE1 N NE1 N Y N 0 -0.152 -2.432 0.094
7 CD1 C CD1 N Y N 0 1.125 -2.028 -0.186
8 CG C CG N Y N 0 1.156 -0.698 -0.364
9 CD2 C CD2 N Y N 0 -0.213 -0.209 -0.182
10 CE3 C CE3 N Y N 0 -0.808 1.053 -0.245
11 CB C CB N N N 0 2.369 0.135 -0.687
12 CA C CA N N N 0 2.958 0.702 0.606
13 NZ N NZ N N N 0 4.141 1.514 0.29
14 HOH H HOH N N N 0 -3.074 2.648 -0.947
15 HH2 H HH2 N N N 0 -3.996 0.166 0.445
16 HZ2 H HZ2 N N N 0 -2.969 -2.058 0.55
17 HNE1 H HNE1 N N N 0 -0.422 -3.348 0.262
18 HD1 H HD1 N N N 0 1.982 -2.683 -0.254
19 HE3 H HE3 N N N 0 -0.211 1.924 -0.469
20 HB1 H 1HB N N N 0 3.114 -0.486 -1.185
21 HB2 H 2HB N N N 0 2.082 0.955 -1.346
22 HA1 H 1HA N N N 0 2.213 1.323 1.103
23 HA2 H 2HA N N N 0 3.246 -0.118 1.264
24 HNZ1 H 1HNZ N N N 0 3.914 2.243 -0.37
25 HNZ2 H 2HNZ N N N 0 4.549 1.9 1.128



SRO : 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 OH CZ3 O C sing 1.36 N N
2 OH HOH O H sing 0.97 N N
3 CZ3 CE3 C C doub 1.38 N Y
4 CZ3 CH2 C C sing 1.39 N Y
5 CH2 CZ2 C C doub 1.38 N Y
6 CH2 HH2 C H sing 1.08 N N
7 CZ2 CE2 C C sing 1.39 N Y
8 CZ2 HZ2 C H sing 1.08 N N
9 CE2 NE1 C N sing 1.38 N Y
10 CE2 CD2 C C doub 1.41 N Y
11 NE1 CD1 N C sing 1.37 N Y
12 NE1 HNE1 N H sing 0.97 N N
13 CD1 CG C C doub 1.34 N Y
14 CD1 HD1 C H sing 1.08 N N
15 CG CB C C sing 1.51 N N
16 CG CD2 C C sing 1.47 N Y
17 CD2 CE3 C C sing 1.4 N Y
18 CE3 HE3 C H sing 1.08 N N
19 CB CA C C sing 1.53 N N
20 CB HB1 C H sing 1.09 N N
21 CB HB2 C H sing 1.09 N N
22 CA NZ C N sing 1.47 N N
23 CA HA1 C H sing 1.09 N N
24 CA HA2 C H sing 1.09 N N
25 NZ HNZ1 N H sing 1.01 N N
26 NZ HNZ2 N H sing 1.01 N N



SRO : Used in PDB Entries

Total Number of PDB Entries: 12
Ligand Code PDB Entry ID Type Total Distinct
SRO 2qeh Open in New Window Bound ligand 1 1
SRO 2ymd Open in New Window Bound ligand 10 1
SRO 3adv Open in New Window Bound ligand 3 1
SRO 3brn Open in New Window Bound ligand 2 1
SRO 3nk1 Open in New Window Bound ligand 1 1
SRO 3q6k Open in New Window Bound ligand 2 1
SRO 4dtw Open in New Window Bound ligand 2 1
SRO 4due Open in New Window Bound ligand 2 1
SRO 4duf Open in New Window Bound ligand 4 1
SRO 5mam Open in New Window Bound ligand 14 1
SRO 5mt3 Open in New Window Bound ligand 12 1
SRO 5mt9 Open in New Window Bound ligand 16 1