Chemical Components in the PDB

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3KJ : Summary

Code

3KJ

One-letter code

X

Molecule name

N~5~-(N-hydroxy-N-methylcarbamimidoyl)-L-ornithine

Systematic names

ProgramVersionName
ACDLabs 12.01 N~5~-(N-hydroxy-N-methylcarbamimidoyl)-L-ornithine
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-5-[(N-methyl-N-oxidanyl-carbamimidoyl)amino]pentanoic acid

Formula

C7 H16 N4 O3

Formal charge

0

Molecular weight

204.227 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCCNC(=[N@H])N(O)C
SMILES CACTVS 3.370 CN(O)C(=N)NCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 CN(C(=N)NCCCC(C(=O)O)N)O
Canonical SMILES CACTVS 3.370 CN(O)C(=N)NCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C(/NCCC[C@@H](C(=O)O)N)\N(C)O

IUPAC InChI

InChI=1S/C7H16N4O3/c1-11(14)7(9)10-4-2-3-5(8)6(12)13/h5,14H,2-4,8H2,1H3,(H2,9,10)(H,12,13)/t5-/m0/s1

IUPAC InChI key

BNNZGZKJTQTHNK-YFKPBYRVSA-N
3KJ

wwPDB Information

Atom count

30 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-07-13

Last modified at

2013-05-10

Status

Released

Obsoleted

Not Assigned



3KJ : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OA1 O OA1 N N N 0 -4.742 -1.015 -1.13
2 C C C N N N 0 -4.341 -0.205 -0.137
3 OA2 O OA2 N N N 0 -5.015 -0.093 0.86
4 CA C CA S N N 0 -3.052 0.563 -0.265
5 N N N N N N 0 -3.062 1.697 0.67
6 CB C CB N N N 0 -1.874 -0.357 0.062
7 CG C CG N N N 0 -0.561 0.386 -0.189
8 CD C CD N N N 0 0.617 -0.534 0.139
9 NE N NE N N N 0 1.875 0.177 -0.101
10 CZ C CZ N N N 0 3.075 -0.453 0.125
11 NH1 N NH1 N N N 0 3.095 -1.684 0.553
12 NH2 N NH2 N N N 0 4.256 0.215 -0.1
13 C1 C C1 N N N 0 5.535 -0.457 0.141
14 OH O OH N N N 0 4.235 1.552 -0.566
15 H1 H H1 N N N 0 -5.576 -1.487 -1.001
16 H2 H H2 N N N 0 -2.95 0.935 -1.285
17 H3 H H3 N N N 0 -3.155 1.378 1.623
18 H4 H H4 N N N 0 -2.236 2.265 0.558
19 H6 H H6 N N N 0 -1.928 -0.657 1.109
20 H7 H H7 N N N 0 -1.918 -1.242 -0.573
21 H8 H H8 N N N 0 -0.507 0.687 -1.235
22 H9 H H9 N N N 0 -0.517 1.271 0.446
23 H10 H H10 N N N 0 0.563 -0.835 1.185
24 H11 H H11 N N N 0 0.573 -1.419 -0.496
25 H12 H H12 N N N 0 1.86 1.094 -0.42
26 H13 H H13 N N N 0 2.262 -2.155 0.712
27 H15 H H15 N N N 0 5.352 -1.472 0.493
28 H16 H H16 N N N 0 6.108 -0.491 -0.786
29 H17 H H17 N N N 0 6.098 0.093 0.895
30 H18 H H18 N N N 0 5.112 1.938 -0.694



3KJ : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OH NH2 O N sing 1.42 N N
2 C1 NH2 C N sing 1.46 N N
3 NH2 CZ N C sing 1.38 N N
4 CZ NH1 C N doub 1.3 N N
5 CZ NE C N sing 1.37 N N
6 CD NE C N sing 1.46 N N
7 CD CG C C sing 1.53 N N
8 OA2 C O C doub 1.21 N N
9 CB CG C C sing 1.53 N N
10 CB CA C C sing 1.53 N N
11 C CA C C sing 1.51 N N
12 C OA1 C O sing 1.34 N N
13 CA N C N sing 1.47 N N
14 OA1 H1 O H sing 0.97 N N
15 CA H2 C H sing 1.09 N N
16 N H3 N H sing 1.01 N N
17 N H4 N H sing 1.01 N N
18 CB H6 C H sing 1.09 N N
19 CB H7 C H sing 1.09 N N
20 CG H8 C H sing 1.09 N N
21 CG H9 C H sing 1.09 N N
22 CD H10 C H sing 1.09 N N
23 CD H11 C H sing 1.09 N N
24 NE H12 N H sing 0.97 N N
25 NH1 H13 N H sing 0.97 N N
26 C1 H15 C H sing 1.09 N N
27 C1 H16 C H sing 1.09 N N
28 C1 H17 C H sing 1.09 N N
29 OH H18 O H sing 0.97 N N



3KJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
3KJ 4fvy Open in New Window Bound ligand 2 1