Chemical Components in the PDB

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J8T : Summary

Code

J8T

One-letter code

X

Molecule name

[(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate

Formula

C6 H14 N O6 P

Formal charge

0

Molecular weight

227.152 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(C)(CO[P](O)(O)=O)[CH](O)C(N)=O
SMILES OpenEye OEToolkits 2.0.7 CC(C)(COP(=O)(O)O)C(C(=O)N)O
Canonical SMILES CACTVS 3.385 CC(C)(CO[P](O)(O)=O)[C@@H](O)C(N)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)(COP(=O)(O)O)[C@H](C(=O)N)O

IUPAC InChI

InChI=1S/C6H14NO6P/c1-6(2,4(8)5(7)9)3-13-14(10,11)12/h4,8H,3H2,1-2H3,(H2,7,9)(H2,10,11,12)/t4-/m0/s1

IUPAC InChI key

UUMQHJQLVJSTLV-BYPYZUCNSA-N
J8T

wwPDB Information

Atom count

28 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-02-11

Last modified at

2020-03-13

Status

Released

Obsoleted

Not Assigned



J8T : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N N N 0 -0.095 -0.1 0.232
2 C5 C C2 N N N 0 -1.202 -0.966 -0.373
3 C6 C C3 N N N 0 -1.221 -0.782 -1.892
4 C7 C C4 N N N 0 -0.939 -2.436 -0.04
5 O3 O O1 N N N 0 2.548 1.743 -0.381
6 O4 O O2 N N N 0 2.717 0.155 1.573
7 O5 O O3 N N N 0 1.167 -0.493 -0.311
8 P1 P P1 N N N 0 2.556 0.208 0.103
9 O6 O O4 N N N 0 -2.581 -0.835 1.607
10 O7 O O5 N N N 0 -2.733 1.69 0.945
11 C8 C C5 R N N 0 -2.553 -0.545 0.208
12 C9 C C6 N N N 0 -2.752 0.934 -0.003
13 N2 N N1 N N N 0 -2.952 1.416 -1.245
14 H1 H H1 N N N 0 -0.282 0.947 -0.005
15 H2 H H2 N N N 0 -0.081 -0.231 1.314
16 H3 H H3 N N N 0 -0.305 -1.191 -2.318
17 H4 H H4 N N N 0 -2.081 -1.305 -2.31
18 H5 H H5 N N N 0 -1.29 0.279 -2.129
19 H6 H H6 N N N 0 -1.005 -2.582 1.038
20 H7 H H7 N N N 0 -1.681 -3.06 -0.538
21 H8 H H8 N N N 0 0.058 -2.713 -0.383
22 H9 H H9 N N N 0 2.446 1.854 -1.336
23 H11 H H11 N N N 0 -1.897 -0.379 2.117
24 H12 H H12 N N N 0 -3.351 -1.094 -0.292
25 H13 H H13 N N N 0 -3.009 2.374 -1.39
26 H14 H H14 N N N 0 -3.04 0.806 -1.994
27 O1 O O6 N N Y 0 3.78 -0.569 -0.599
28 H10 H H10 N N N 0 4.649 -0.201 -0.393



J8T : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 P1 O P sing 1.61 N N
2 P1 O4 P O doub 1.48 N N
3 P1 O5 P O sing 1.61 N N
4 O5 C4 O C sing 1.43 N N
5 C4 C5 C C sing 1.53 N N
6 C7 C5 C C sing 1.53 N N
7 C5 C8 C C sing 1.53 N N
8 C5 C6 C C sing 1.53 N N
9 C8 O6 C O sing 1.43 N N
10 C8 C9 C C sing 1.51 N N
11 O7 C9 O C doub 1.21 N N
12 C9 N2 C N sing 1.35 N N
13 C4 H1 C H sing 1.09 N N
14 C4 H2 C H sing 1.09 N N
15 C6 H3 C H sing 1.09 N N
16 C6 H4 C H sing 1.09 N N
17 C6 H5 C H sing 1.09 N N
18 C7 H6 C H sing 1.09 N N
19 C7 H7 C H sing 1.09 N N
20 C7 H8 C H sing 1.09 N N
21 O3 H9 O H sing 0.97 N N
22 O6 H11 O H sing 0.97 N N
23 C8 H12 C H sing 1.09 N N
24 N2 H13 N H sing 0.97 N N
25 N2 H14 N H sing 0.97 N N
26 P1 O1 P O sing 1.61 N N
27 O1 H10 O H sing 0.97 N N



J8T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
J8T 6ql6 Open in New Window Bound ligand 6 1