Chemical Components in the PDB

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5HG : Summary

Code

5HG

One-letter code

X

Molecule name

{[2-(6-AMINO-9H-PURIN-9-YL)ETHOXY]METHYL}PHOSPHONIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 {[2-(6-amino-9H-purin-9-yl)ethoxy]methyl}phosphonic acid
OpenEye OEToolkits 1.5.0 2-(6-aminopurin-9-yl)ethoxymethylphosphonic acid

Formula

C8 H12 N5 O4 P

Formal charge

0

Molecular weight

273.186 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)COCCn1c2ncnc(c2nc1)N
SMILES CACTVS 3.341 Nc1ncnc2n(CCOC[P](O)(O)=O)cnc12
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)CCOCP(=O)(O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(CCOC[P](O)(O)=O)cnc12
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)CCOCP(=O)(O)O)N

IUPAC InChI

InChI=1S/C8H12N5O4P/c9-7-6-8(11-3-10-7)13(4-12-6)1-2-17-5-18(14,15)16/h3-4H,1-2,5H2,(H2,9,10,11)(H2,14,15,16)

IUPAC InChI key

SUPKOOSCJHTBAH-UHFFFAOYSA-N
5HG

wwPDB Information

Atom count

30 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-02-23

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



5HG : 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 O36 O O36 N N N 0 -4.598 -0.648 0.829
2 P30 P P30 N N N 0 -3.89 -0.231 -0.401
3 O32 O O32 N N N 0 -4.938 -0.142 -1.62
4 O34 O O34 N N N 0 -2.746 -1.308 -0.754
5 C28 C C28 N N N 0 -3.125 1.403 -0.137
6 O26 O O26 N N N 0 -2.194 1.324 0.945
7 C24 C C24 N N N 0 -1.039 0.645 0.448
8 C22 C C22 N N N 0 0.002 0.526 1.562
9 N17 N N17 N Y N 0 1.186 -0.17 1.053
10 C15 C C15 N Y N 0 1.446 -1.504 1.161
11 N13 N N13 N Y N 0 2.585 -1.782 0.597
12 C2 C C2 N Y N 0 3.125 -0.648 0.088
13 C3 C C3 N Y N 0 2.236 0.4 0.379
14 N4 N N4 N Y N 0 2.54 1.633 -0.014
15 C5 C C5 N Y N 0 3.659 1.873 -0.664
16 N6 N N6 N Y N 0 4.528 0.921 -0.955
17 C1 C C1 N Y N 0 4.31 -0.341 -0.602
18 N20 N N20 N N N 0 5.226 -1.331 -0.911
19 HO32 H HO32 N N N 0 -5.319 -1.024 -1.726
20 HO34 H HO34 N N N 0 -2.31 -0.999 -1.56
21 H281 H 1H28 N N N 0 -3.899 2.132 0.102
22 H282 H 2H28 N N N 0 -2.603 1.711 -1.043
23 H241 H 1H24 N N N 0 -0.618 1.207 -0.385
24 H242 H 2H24 N N N 0 -1.322 -0.351 0.107
25 H221 H 1H22 N N N 0 -0.42 -0.036 2.395
26 H222 H 2H22 N N N 0 0.285 1.522 1.903
27 H15 H H15 N N N 0 0.801 -2.224 1.644
28 H5 H H5 N N N 0 3.876 2.886 -0.969
29 H201 H 1H20 N N N 0 6.038 -1.107 -1.392
30 H202 H 2H20 N N N 0 5.057 -2.249 -0.645



5HG : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O36 P30 O P doub 1.48 N N
2 P30 O32 P O sing 1.61 N N
3 P30 O34 P O sing 1.61 N N
4 P30 C28 P C sing 1.82 N N
5 O32 HO32 O H sing 0.97 N N
6 O34 HO34 O H sing 0.97 N N
7 C28 O26 C O sing 1.43 N N
8 C28 H281 C H sing 1.09 N N
9 C28 H282 C H sing 1.09 N N
10 O26 C24 O C sing 1.43 N N
11 C24 C22 C C sing 1.53 N N
12 C24 H241 C H sing 1.09 N N
13 C24 H242 C H sing 1.09 N N
14 C22 N17 C N sing 1.46 N N
15 C22 H221 C H sing 1.09 N N
16 C22 H222 C H sing 1.09 N N
17 N17 C15 N C sing 1.36 N Y
18 N17 C3 N C sing 1.37 N Y
19 C15 N13 C N doub 1.3 N Y
20 C15 H15 C H sing 1.08 N N
21 N13 C2 N C sing 1.36 N Y
22 C2 C3 C C sing 1.4 N Y
23 C2 C1 C C doub 1.41 N Y
24 C3 N4 C N doub 1.33 N Y
25 N4 C5 N C sing 1.32 N Y
26 C5 N6 C N doub 1.32 N Y
27 C5 H5 C H sing 1.08 N N
28 N6 C1 N C sing 1.33 N Y
29 C1 N20 C N sing 1.38 N N
30 N20 H201 N H sing 0.97 N N
31 N20 H202 N H sing 0.97 N N



5HG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5HG 2g1a Open in New Window Bound ligand 2 1