Chemical Components in the PDB

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CIR : Summary

Code

CIR

One-letter code

R

Molecule name

CITRULLINE

Systematic names

ProgramVersionName
ACDLabs 12.01 N~5~-carbamoyl-L-ornithine
OpenEye OEToolkits 1.7.0 (2S)-5-(aminocarbonylamino)-2-azanyl-pentanoic acid

Formula

C6 H13 N3 O3

Formal charge

0

Molecular weight

175.186 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCCNC(=O)N
SMILES CACTVS 3.370 N[CH](CCCNC(N)=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.0 C(CC(C(=O)O)N)CNC(=O)N
Canonical SMILES CACTVS 3.370 N[C@@H](CCCNC(N)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 C(C[C@@H](C(=O)O)N)CNC(=O)N

IUPAC InChI

InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1

IUPAC InChI key

RHGKLRLOHDJJDR-BYPYZUCNSA-N
CIR

wwPDB Information

Atom count

25 (12 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

ARG

Defined at

1999-07-08

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



CIR : 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 C C C1 N N N 0 3.505 0.297 -0.037
2 O O O1 N N N 0 4.165 -0.036 0.919
3 OXT O O2 N N Y 0 3.886 1.346 -0.783
4 CA C C2 S N N 0 2.258 -0.469 -0.396
5 N N N2 N N N 0 2.308 -1.801 0.221
6 C3 C C3 N N N 0 1.03 0.286 0.119
7 C4 C C4 N N N 0 -0.24 -0.426 -0.352
8 C5 C C5 N N N 0 -1.467 0.329 0.162
9 N6 N N6 N N N 0 -2.684 -0.352 -0.289
10 C7 C C7 N N N 0 -3.894 0.137 0.047
11 O7 O O7 N N N 0 -3.976 1.143 0.724
12 N8 N N8 N N N 0 -5.012 -0.49 -0.368
13 HXT H HO2 N N Y 0 4.695 1.804 -0.516
14 HA H H2 N N N 0 2.194 -0.572 -1.479
15 H2 H HN21 N N Y 0 2.367 -1.733 1.226
16 H H HN22 N N N 0 1.513 -2.358 -0.057
17 H31 H H31 N N N 0 1.05 0.311 1.208
18 H32 H H32 N N N 0 1.041 1.304 -0.269
19 H41 H H41 N N N 0 -0.259 -0.452 -1.442
20 H42 H H42 N N N 0 -0.251 -1.444 0.035
21 H51 H H51 N N N 0 -1.448 0.354 1.251
22 H52 H H52 N N N 0 -1.457 1.347 -0.226
23 HN6 H HN6 N N N 0 -2.618 -1.156 -0.829
24 HN81 H HN81 N N N 0 -4.947 -1.293 -0.908
25 HN82 H HN82 N N Y 0 -5.884 -0.138 -0.126



CIR : 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 C O C O doub 1.21 N N
2 C OXT C O sing 1.34 N N
3 C CA C C sing 1.51 N N
4 OXT HXT O H sing 0.97 N N
5 CA N C N sing 1.47 N N
6 CA C3 C C sing 1.53 N N
7 CA HA C H sing 1.09 N N
8 N H2 N H sing 1.01 N N
9 N H N H sing 1.01 N N
10 C3 C4 C C sing 1.53 N N
11 C3 H31 C H sing 1.09 N N
12 C3 H32 C H sing 1.09 N N
13 C4 C5 C C sing 1.53 N N
14 C4 H41 C H sing 1.09 N N
15 C4 H42 C H sing 1.09 N N
16 C5 N6 C N sing 1.47 N N
17 C5 H51 C H sing 1.09 N N
18 C5 H52 C H sing 1.09 N N
19 N6 C7 N C sing 1.35 N N
20 N6 HN6 N H sing 0.97 N N
21 C7 O7 C O doub 1.22 N N
22 C7 N8 C N sing 1.35 N N
23 N8 HN81 N H sing 0.97 N N
24 N8 HN82 N H sing 0.97 N N



CIR : Used in PDB Entries

Total Number of PDB Entries: 65
Ligand Code PDB Entry ID Type Total Distinct
CIR 1h70 Open in New Window Bound ligand 1 1
CIR 1j1z Open in New Window Bound ligand 4 1
CIR 1j21 Open in New Window Bound ligand 4 1
CIR 1k97 Open in New Window Bound ligand 1 1
CIR 1kod Open in New Window Bound ligand 1 1
CIR 1kp3 Open in New Window Bound ligand 2 1
CIR 1lxy Open in New Window Bound ligand 2 1
CIR 1ol1 Open in New Window Polymer component 4 2
CIR 1qr3 Open in New Window Polymer component 1 1
CIR 2c6z Open in New Window Bound ligand 1 1
CIR 2jai Open in New Window Bound ligand 1 1
CIR 2nz2 Open in New Window Bound ligand 1 1
CIR 2w65 Open in New Window Polymer component 2 1
CIR 3b3i Open in New Window Polymer component 1 1
CIR 3b6s Open in New Window Polymer component 1 1
CIR 3dtx Open in New Window Polymer component 2 2
CIR 3ft2 Open in New Window Polymer component 1 1
CIR 3hcv Open in New Window Polymer component 2 2
CIR 3oe0 Open in New Window Polymer component 1 1
CIR 3zop Open in New Window Polymer component 6 1
CIR 3zp4 Open in New Window Polymer component 6 1
CIR 3zp7 Open in New Window Polymer component 6 1
CIR 4gvy Open in New Window Bound ligand 1 1
CIR 4jqo Open in New Window Bound ligand 3 1
CIR 4mcy Open in New Window Polymer component 1 1
CIR 4mcz Open in New Window Polymer component 1 1
CIR 4md0 Open in New Window Polymer component 3 3
CIR 4md4 Open in New Window Polymer component 2 2
CIR 4md5 Open in New Window Polymer component 1 1
CIR 4mdi Open in New Window Polymer component 1 1
CIR 5iv2 Open in New Window Polymer component 2 1
CIR 5ivz Open in New Window Polymer component 2 1
CIR 5jlz Open in New Window Polymer component 2 1
CIR 5mu0 Open in New Window Polymer component 8 1
CIR 5mub Open in New Window Polymer component 8 1
CIR 5mv4 Open in New Window Polymer component 8 1
CIR 5nig Open in New Window Polymer component 1 1
CIR 5ock Open in New Window Polymer component 2 2
CIR 5ocx Open in New Window Polymer component 1 1
CIR 5ocy Open in New Window Polymer component 1 1
CIR 5uhr Open in New Window Polymer component 4 1
CIR 6ati Open in New Window Polymer component 2 1
CIR 6atz Open in New Window Polymer component 2 1
CIR 6bij Open in New Window Polymer component 2 2
CIR 6bil Open in New Window Polymer component 1 1
CIR 6bin Open in New Window Polymer component 1 1
CIR 6bir Open in New Window Polymer component 1 1
CIR 6biv Open in New Window Polymer component 1 1
CIR 6bix Open in New Window Polymer component 1 1
CIR 6biz Open in New Window Polymer component 2 2
CIR 6eqv Open in New Window Polymer component 1 1
CIR 6o34 Open in New Window Polymer component 1 1
CIR 6v0y Open in New Window Polymer component 2 2
CIR 6v13 Open in New Window Polymer component 1 1
CIR 6v15 Open in New Window Polymer component 2 2
CIR 6v18 Open in New Window Polymer component 1 1
CIR 6v19 Open in New Window Polymer component 2 2
CIR 6v1a Open in New Window Polymer component 1 1
CIR 6yxk Open in New Window Polymer component 2 2
CIR 6yxm Open in New Window Polymer component 1 1
CIR 6zjg Open in New Window Polymer component 1 1
CIR 7nzh Open in New Window Polymer component 4 2
CIR 8trl Open in New Window Polymer component 2 1
CIR 8trq Open in New Window Polymer component 1 1
CIR 8trr Open in New Window Polymer component 2 1