Chemical Components in the PDB

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SEC : Summary

Code

SEC

One-letter code

U

Molecule name

SELENOCYSTEINE

Systematic names

ProgramVersionName
ACDLabs 12.01 3-selanyl-L-alanine
OpenEye OEToolkits 1.7.6 (2R)-2-azanyl-3-selanyl-propanoic acid

Formula

C3 H7 N O2 Se

Formal charge

0

Molecular weight

168.053 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)C[SeH]
SMILES CACTVS 3.370 N[CH](C[SeH])C(O)=O
SMILES OpenEye OEToolkits 1.7.6 C(C(C(=O)O)N)[SeH]
Canonical SMILES CACTVS 3.370 N[C@@H](C[SeH])C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C([C@@H](C(=O)O)N)[SeH]

IUPAC InChI

InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1

IUPAC InChI key

ZKZBPNGNEQAJSX-REOHCLBHSA-N
SEC

wwPDB Information

Atom count

14 (7 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



SEC : Atoms of Molecule

Total Number of Atoms: 14
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 -0.783 1.676 -0.339
2 CA C CA R N N 0 -0.938 0.217 -0.405
3 CB C CB N N N 0 0.042 -0.445 0.565
4 SE SE SE N N N 0 1.879 -0.092 -0.02
5 C C C N N N 0 -2.349 -0.156 -0.027
6 O O O N N N 0 -3.03 0.619 0.602
7 OXT O OXT N N Y 0 -2.848 -1.348 -0.389
8 H H HN1 N N N 0 -1.373 2.134 -1.017
9 H2 H HN2 N N Y 0 -0.969 2.018 0.592
10 HA H HA N N N 0 -0.732 -0.125 -1.419
11 HB2 H HB1 N N N 0 -0.105 -0.037 1.565
12 HB3 H HB2 N N N 0 -0.134 -1.521 0.582
13 HE H HE N N N 0 2.691 -0.839 1.084
14 HXT H HXT N N Y 0 -3.757 -1.542 -0.123



SEC : Chemical Bonds

Total Number of Bonds: 13
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 CA CB C C sing 1.53 N N
5 CA C C C sing 1.51 N N
6 CA HA C H sing 1.09 N N
7 CB SE C SE sing 1.96 N N
8 CB HB2 C H sing 1.09 N N
9 CB HB3 C H sing 1.09 N N
10 SE HE SE H sing 1.56 N N
11 C O C O doub 1.21 N N
12 C OXT C O sing 1.34 N N
13 OXT HXT O H sing 0.97 N N



SEC : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
SEC 1kmk Open in New Window Bound ligand 1 1
SEC 5fex Open in New Window Bound ligand 1 1
SEC 5lzb Open in New Window Bound ligand 1 1
SEC 5lzc Open in New Window Bound ligand 1 1
SEC 5lzd Open in New Window Bound ligand 1 1
SEC 5w2v Open in New Window Bound ligand 1 1
SEC 5w32 Open in New Window Bound ligand 1 1
SEC 5w3c Open in New Window Bound ligand 1 1
SEC 7yvd Open in New Window Bound ligand 3 1