Chemical Components in the PDB

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0TK : Summary

Code

0TK

One-letter code

X

Molecule name

(2R)-2,5-diaminopentanoyl dihydrogen phosphate

Synonyms

phosphorylated D-ornithine

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R)-2,5-diaminopentanoyl dihydrogen phosphate
OpenEye OEToolkits 1.7.6 phosphono (2R)-2,5-bis(azanyl)pentanoate

Formula

C5 H13 N2 O5 P

Formal charge

0

Molecular weight

212.141 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(OC(=O)C(N)CCCN)(O)O
SMILES CACTVS 3.370 NCCC[CH](N)C(=O)O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.6 C(CC(C(=O)OP(=O)(O)O)N)CN
Canonical SMILES CACTVS 3.370 NCCC[C@@H](N)C(=O)O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C(C[C@H](C(=O)OP(=O)(O)O)N)CN

IUPAC InChI

InChI=1S/C5H13N2O5P/c6-3-1-2-4(7)5(8)12-13(9,10)11/h4H,1-3,6-7H2,(H2,9,10,11)/t4-/m1/s1

IUPAC InChI key

MNDHJWIHMSHXOW-SCSAIBSYSA-N
0TK

wwPDB Information

Atom count

26 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-06-06

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



0TK : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -1.115 0.864 -0.51
2 C2 C C2 N N N 0 -2.001 -0.142 0.228
3 C3 C C3 N N N 0 -3.43 -0.053 -0.31
4 O12 O O12 N N N 0 3.347 -1.562 -0.889
5 P11 P P11 N N N 0 2.582 -0.412 -0.062
6 O13 O O13 N N N 0 2.583 -0.786 1.504
7 O14 O O14 N N N 0 3.274 0.882 -0.261
8 O10 O O10 N N N 0 1.064 -0.295 -0.585
9 C8 C C8 N N N 0 0.316 0.692 -0.068
10 O9 O O9 N N N 0 0.789 1.443 0.752
11 N7 N N7 N N N 0 -1.562 2.229 -0.201
12 C4 C C4 N N N 0 -4.316 -1.059 0.427
13 N5 N N5 N N N 0 -5.688 -0.974 -0.089
14 H1 H H1 N N N 0 -1.186 0.692 -1.584
15 H2 H H2 N N N 0 -1.615 -1.149 0.07
16 H3 H H3 N N N 0 -1.999 0.085 1.294
17 H4 H H4 N N N 0 -3.816 0.954 -0.153
18 H5 H H5 N N N 0 -3.432 -0.28 -1.376
19 H6 H H6 N N N 0 4.269 -1.688 -0.626
20 H7 H H7 N N N 0 2.145 -1.624 1.708
21 H8 H H8 N N N 0 -1.505 2.413 0.789
22 H9 H H9 N N N 0 -1.034 2.91 -0.726
23 H11 H H11 N N N 0 -3.93 -2.067 0.27
24 H12 H H12 N N N 0 -4.314 -0.832 1.493
25 H13 H H13 N N N 0 -5.709 -1.117 -1.088
26 H14 H H14 N N N 0 -6.294 -1.63 0.382



0TK : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N7 C1 N C sing 1.47 N N
2 O9 C8 O C doub 1.21 N N
3 C1 C2 C C sing 1.53 N N
4 C1 C8 C C sing 1.51 N N
5 C3 C2 C C sing 1.53 N N
6 C3 C4 C C sing 1.53 N N
7 C8 O10 C O sing 1.34 N N
8 C4 N5 C N sing 1.47 N N
9 O14 P11 O P doub 1.48 N N
10 O10 P11 O P sing 1.61 N N
11 P11 O12 P O sing 1.61 N N
12 P11 O13 P O sing 1.61 N N
13 C1 H1 C H sing 1.09 N N
14 C2 H2 C H sing 1.09 N N
15 C2 H3 C H sing 1.09 N N
16 C3 H4 C H sing 1.09 N N
17 C3 H5 C H sing 1.09 N N
18 O12 H6 O H sing 0.97 N N
19 O13 H7 O H sing 0.97 N N
20 N7 H8 N H sing 1.01 N N
21 N7 H9 N H sing 1.01 N N
22 C4 H11 C H sing 1.09 N N
23 C4 H12 C H sing 1.09 N N
24 N5 H13 N H sing 1.01 N N
25 N5 H14 N H sing 1.01 N N



0TK : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0TK 4ffo Open in New Window Bound ligand 1 1