Chemical Components in the PDB

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6MS : Summary

Code

6MS

One-letter code

X

Molecule name

[6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)hexyl]phosphonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 [6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)hexyl]phosphonic acid
OpenEye OEToolkits 2.0.4 6-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)hexylphosphonic acid

Formula

C11 H18 N5 O4 P

Formal charge

0

Molecular weight

315.265 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(CCCCCP(O)(=O)O)n2c1N=C(NC(=O)c1nc2)N
SMILES CACTVS 3.385 NC1=Nc2n(CCCCCC[P](O)(O)=O)cnc2C(=O)N1
SMILES OpenEye OEToolkits 2.0.4 c1nc2c(n1CCCCCCP(=O)(O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(CCCCCC[P](O)(O)=O)cnc2C(=O)N1
Canonical SMILES OpenEye OEToolkits 2.0.4 c1nc2c(n1CCCCCCP(=O)(O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C11H18N5O4P/c12-11-14-9-8(10(17)15-11)13-7-16(9)5-3-1-2-4-6-21(18,19)20/h7H,1-6H2,(H2,18,19,20)(H3,12,14,15,17)

IUPAC InChI key

CULYTKHWSUTBGY-UHFFFAOYSA-N
6MS

wwPDB Information

Atom count

39 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-05-09

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



6MS : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C12 C C1 N N N 0 1.272 1.111 -1.149
2 P18 P P1 N N N 0 -6.225 -0.29 0.147
3 O01 O O1 N N N 0 6.716 0.388 1.088
4 C02 C C2 N N N 0 5.703 -0.071 0.589
5 N03 N N1 N N N 0 5.588 -1.396 0.352
6 C04 C C3 N N N 0 4.451 -1.899 -0.207
7 N05 N N2 N N N 0 4.362 -3.25 -0.436
8 N06 N N3 N N N 0 3.437 -1.129 -0.532
9 C07 C C4 N Y N 0 3.479 0.193 -0.327
10 C08 C C5 N Y N 0 4.618 0.769 0.248
11 N09 N N4 N Y N 0 4.391 2.103 0.339
12 C10 C C6 N Y N 0 3.211 2.372 -0.136
13 N11 N N5 N Y N 0 2.607 1.222 -0.555
14 C13 C C7 N N N 0 0.256 0.768 -0.058
15 C14 C C8 N N N 0 -1.138 0.651 -0.677
16 C15 C C9 N N N 0 -2.154 0.308 0.414
17 C16 C C10 N N N 0 -3.548 0.192 -0.206
18 C17 C C11 N N N 0 -4.564 -0.152 0.885
19 O19 O O2 N N N 0 -6.681 1.145 -0.422
20 O20 O O3 N N N 0 -6.193 -1.272 -0.96
21 O21 O O4 N N N 0 -7.272 -0.779 1.268
22 H1 H H1 N N N 0 1.0 2.06 -1.612
23 H2 H H2 N N N 0 1.274 0.325 -1.904
24 H3 H H3 N N N 0 5.101 -3.831 -0.2
25 H4 H H4 N N N 0 3.559 -3.622 -0.833
26 H6 H H6 N N N 0 2.772 3.358 -0.186
27 H7 H H7 N N N 0 0.527 -0.181 0.406
28 H8 H H8 N N N 0 0.254 1.554 0.697
29 H9 H H9 N N N 0 -1.41 1.6 -1.141
30 H10 H H10 N N N 0 -1.136 -0.135 -1.432
31 H11 H H11 N N N 0 -1.883 -0.64 0.878
32 H12 H H12 N N N 0 -2.157 1.094 1.169
33 H13 H H13 N N N 0 -3.82 1.14 -0.669
34 H14 H H14 N N N 0 -3.546 -0.594 -0.961
35 H15 H H15 N N N 0 -4.567 0.634 1.64
36 H16 H H16 N N N 0 -4.293 -1.1 1.349
37 H17 H H17 N N N 0 -6.724 1.839 0.25
38 H18 H H18 N N N 0 -8.178 -0.875 0.945
39 H5 H H5 N N N 0 6.318 -1.993 0.581



6MS : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O20 P18 O P doub 1.48 N N
2 O21 P18 O P sing 1.61 N N
3 P18 C17 P C sing 1.82 N N
4 P18 O19 P O sing 1.61 N N
5 C16 C17 C C sing 1.53 N N
6 C16 C15 C C sing 1.53 N N
7 C14 C15 C C sing 1.53 N N
8 C14 C13 C C sing 1.53 N N
9 C12 C13 C C sing 1.53 N N
10 C12 N11 C N sing 1.47 N N
11 N11 C10 N C sing 1.36 N Y
12 N11 C07 N C sing 1.37 N Y
13 C10 N09 C N doub 1.3 N Y
14 C07 N06 C N sing 1.34 N N
15 C07 C08 C C doub 1.4 N Y
16 N06 C04 N C doub 1.31 N N
17 N09 C08 N C sing 1.36 N Y
18 C08 C02 C C sing 1.41 N N
19 C04 N05 C N sing 1.37 N N
20 C04 N03 C N sing 1.36 N N
21 C02 N03 C N sing 1.35 N N
22 C02 O01 C O doub 1.22 N N
23 C12 H1 C H sing 1.09 N N
24 C12 H2 C H sing 1.09 N N
25 N05 H3 N H sing 0.97 N N
26 N05 H4 N H sing 0.97 N N
27 C10 H6 C H sing 1.08 N N
28 C13 H7 C H sing 1.09 N N
29 C13 H8 C H sing 1.09 N N
30 C14 H9 C H sing 1.09 N N
31 C14 H10 C H sing 1.09 N N
32 C15 H11 C H sing 1.09 N N
33 C15 H12 C H sing 1.09 N N
34 C16 H13 C H sing 1.09 N N
35 C16 H14 C H sing 1.09 N N
36 C17 H15 C H sing 1.09 N N
37 C17 H16 C H sing 1.09 N N
38 O19 H17 O H sing 0.97 N N
39 O21 H18 O H sing 0.97 N N
40 N03 H5 N H sing 0.97 N N



6MS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6MS 5jsq Open in New Window Bound ligand 2 1