Chemical Components in the PDB

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2D8 : Summary

Code

2D8

One-letter code

X

Molecule name

(2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid
OpenEye OEToolkits 1.7.6 (2R)-3-[[(1S)-1-azanylethyl]-oxidanyl-phosphoryl]-2-methyl-propanoic acid

Formula

C6 H14 N O4 P

Formal charge

0

Molecular weight

195.153 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(C(N)C)CC(C(=O)O)C
SMILES CACTVS 3.385 C[CH](N)[P](O)(=O)C[CH](C)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(CP(=O)(C(C)N)O)C(=O)O
Canonical SMILES CACTVS 3.385 C[C@@H](N)[P](O)(=O)C[C@H](C)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@H](CP(=O)([C@@H](C)N)O)C(=O)O

IUPAC InChI

InChI=1S/C6H14NO4P/c1-4(6(8)9)3-12(10,11)5(2)7/h4-5H,3,7H2,1-2H3,(H,8,9)(H,10,11)/t4-,5-/m0/s1

IUPAC InChI key

XXVGIEKADYFHOF-WHFBIAKZSA-N
2D8

wwPDB Information

Atom count

26 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-09-25

Last modified at

2013-10-04

Status

Released

Obsoleted

Not Assigned



2D8 : 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 C4 C C4 N N N 0 0.45 -0.589 -0.065
2 C5 C C5 R N N 0 1.631 0.377 0.051
3 C6 C C6 N N N 0 2.912 -0.407 0.174
4 C7 C C7 N N N 0 1.692 1.26 -1.197
5 N1 N N1 N N N 0 -2.57 -1.545 -1.056
6 P P P N N N 0 -1.105 0.315 0.233
7 C1 C C1 N N N 0 -3.804 -0.103 0.491
8 C2 C C2 S N N 0 -2.498 -0.861 0.242
9 O31 O O31 N N N 0 -1.033 1.004 1.54
10 O32 O O32 N N N 0 -1.327 1.401 -0.935
11 O61 O O61 N N N 0 4.084 0.235 0.289
12 O62 O O62 N N N 0 2.883 -1.615 0.17
13 H1 H H1 N N N 0 0.433 -1.023 -1.064
14 H2 H H2 N N N 0 0.556 -1.383 0.674
15 H3 H H3 N N N 0 1.503 1.004 0.934
16 H4 H H4 N N N 0 0.766 1.828 -1.286
17 H5 H H5 N N N 0 2.534 1.949 -1.114
18 H6 H H6 N N N 0 1.821 0.634 -2.079
19 H7 H H7 N N N 0 -2.709 -0.885 -1.806
20 H8 H H8 N N N 0 -1.746 -2.105 -1.216
21 H10 H H10 N N N 0 -4.637 -0.805 0.496
22 H11 H H11 N N N 0 -3.751 0.405 1.454
23 H12 H H12 N N N 0 -3.954 0.633 -0.3
24 H13 H H13 N N N 0 -2.348 -1.596 1.032
25 H14 H H14 N N N 0 -1.383 1.019 -1.822
26 H15 H H15 N N N 0 4.879 -0.311 0.366



2D8 : 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 C1 C2 C C sing 1.53 N N
2 C2 N1 C N sing 1.47 N N
3 C2 P C P sing 1.82 N N
4 O62 C6 O C doub 1.21 N N
5 C4 P C P sing 1.82 N N
6 C4 C5 C C sing 1.53 N N
7 P O31 P O doub 1.48 N N
8 P O32 P O sing 1.61 N N
9 C6 C5 C C sing 1.51 N N
10 C6 O61 C O sing 1.34 N N
11 C7 C5 C C sing 1.53 N N
12 C4 H1 C H sing 1.09 N N
13 C4 H2 C H sing 1.09 N N
14 C5 H3 C H sing 1.09 N N
15 C7 H4 C H sing 1.09 N N
16 C7 H5 C H sing 1.09 N N
17 C7 H6 C H sing 1.09 N N
18 N1 H7 N H sing 1.01 N N
19 N1 H8 N H sing 1.01 N N
20 C1 H10 C H sing 1.09 N N
21 C1 H11 C H sing 1.09 N N
22 C1 H12 C H sing 1.09 N N
23 C2 H13 C H sing 1.09 N N
24 O32 H14 O H sing 0.97 N N
25 O61 H15 O H sing 0.97 N N



2D8 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
2D8 4muq Open in New Window Bound ligand 1 1
2D8 4mus Open in New Window Bound ligand 2 1