Chemical Components in the PDB

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ORD : Summary

Code

ORD

One-letter code

X

Molecule name

D-ORNITHINE

Systematic names

ProgramVersionName
ACDLabs 10.04 D-ornithine
OpenEye OEToolkits 1.6.1 (2R)-2,5-diaminopentanoic acid

Formula

C5 H12 N2 O2

Formal charge

0

Molecular weight

132.161 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N)CCCN
SMILES CACTVS 3.352 NCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.6.1 C(CC(C(=O)O)N)CN
Canonical SMILES CACTVS 3.352 NCCC[C@@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.6.1 C(C[C@H](C(=O)O)N)CN

IUPAC InChI

InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1

IUPAC InChI key

AHLPHDHHMVZTML-SCSAIBSYSA-N
ORD

wwPDB Information

Atom count

21 (9 without Hydrogen)

Polymer type

Amino Acid

Type description

D-PEPTIDE LINKING

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2010-09-08

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



ORD : Atoms of Molecule

Total Number of Atoms: 21
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 -0.758 1.774 0.274
2 CA C CA R N N 0 -0.782 0.321 0.488
3 CB C CB N N N 0 0.368 -0.327 -0.286
4 CG C CG N N N 0 1.703 0.146 0.294
5 CD C CD N N N 0 2.853 -0.502 -0.479
6 NE N NE N N N 0 4.135 -0.049 0.078
7 O O O N N N 0 -2.762 0.392 -0.787
8 OXT O OXT N N Y 0 -2.518 -1.434 0.435
9 C C C N N N 0 -2.093 -0.237 -0.002
10 H H H N N N 0 -0.86 1.997 -0.705
11 H2 H H2 N N Y 0 -1.468 2.232 0.825
12 HA H HA N N N 0 -0.67 0.108 1.551
13 HB2 H HB2 N N N 0 0.299 -1.411 -0.2
14 HB3 H HB3 N N N 0 0.307 -0.041 -1.336
15 HG2 H HG2 N N N 0 1.773 1.23 0.208
16 HG3 H HG3 N N N 0 1.765 -0.14 1.344
17 HD2 H HD2 N N N 0 2.783 -1.587 -0.393
18 HD3 H HD3 N N N 0 2.792 -0.217 -1.529
19 HE1 H HE1 N N N 0 4.189 -0.245 1.066
20 HE2 H HE2 N N N 0 4.911 -0.463 -0.416
21 HXT H HXT N N Y 0 -3.365 -1.75 0.093



ORD : Chemical Bonds

Total Number of Bonds: 20
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 CA CB C C sing 1.53 N N
3 CA C C C sing 1.51 N N
4 CB CG C C sing 1.53 N N
5 CG CD C C sing 1.53 N N
6 CD NE C N sing 1.47 N N
7 C O C O doub 1.21 N N
8 C OXT C O sing 1.34 N N
9 N H N H sing 1.01 N N
10 N H2 N H sing 1.01 N N
11 CA HA C H sing 1.09 N N
12 CB HB2 C H sing 1.09 N N
13 CB HB3 C H sing 1.09 N N
14 CG HG2 C H sing 1.09 N N
15 CG HG3 C H sing 1.09 N N
16 CD HD2 C H sing 1.09 N N
17 CD HD3 C H sing 1.09 N N
18 NE HE1 N H sing 1.01 N N
19 NE HE2 N H sing 1.01 N N
20 OXT HXT O H sing 0.97 N N



ORD : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
ORD 1dsr Open in New Window Polymer component 2 2
ORD 4ffn Open in New Window Bound ligand 1 1
ORD 4k7t Open in New Window Polymer component 1 1
ORD 5f1w Open in New Window Polymer component 12 2
ORD 6cae Open in New Window Polymer component 3 1
ORD 8apz Open in New Window Bound ligand 2 1
ORD 8g97 Open in New Window Bound ligand 2 1