Chemical Components in the PDB

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8QI : Summary

Code

8QI

One-letter code

X

Molecule name

({(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2S)-2-hydroxy-2-phosphonoethoxy]propoxy}methyl)phosphonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 ({(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2S)-2-hydroxy-2-phosphonoethoxy]propoxy}methyl)phosphonic acid
OpenEye OEToolkits 2.0.7 [(2~{S})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]propoxy]methylphosphonic acid

Formula

C11 H19 N5 O10 P2

Formal charge

0

Molecular weight

443.244 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)COCC(OCC(O)P(=O)(O)O)Cn1cnc2c1N=C(N)NC2=O
SMILES CACTVS 3.385 NC1=Nc2n(C[CH](COC[P](O)(O)=O)OC[CH](O)[P](O)(O)=O)cnc2C(=O)N1
SMILES OpenEye OEToolkits 2.0.7 c1nc2c(n1CC(COCP(=O)(O)O)OCC(O)P(=O)(O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(C[C@@H](COC[P](O)(O)=O)OC[C@@H](O)[P](O)(O)=O)cnc2C(=O)N1
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc2c(n1C[C@@H](COCP(=O)(O)O)OC[C@@H](O)P(=O)(O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C11H19N5O10P2/c12-11-14-9-8(10(18)15-11)13-4-16(9)1-6(2-25-5-27(19,20)21)26-3-7(17)28(22,23)24/h4,6-7,17H,1-3,5H2,(H2,19,20,21)(H2,22,23,24)(H3,12,14,15,18)/t6-,7-/m0/s1

IUPAC InChI key

BCERVIXRVPEQOK-BQBZGAKWSA-N
8QI

wwPDB Information

Atom count

47 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-09-24

Last modified at

2022-02-25

Status

Released

Obsoleted

Not Assigned



8QI : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 -0.902 -0.263 -0.633
2 C17 C C2 N N N 0 -1.605 2.092 0.255
3 C24 C C3 N Y N 0 2.914 2.802 1.074
4 C26 C C4 N Y N 0 4.173 1.171 0.4
5 C02 C C5 N N N 0 3.716 -0.812 -1.394
6 C05 C C6 N Y N 0 2.955 1.066 -0.283
7 C07 C C7 N N N 0 0.816 2.412 -0.275
8 C08 C C8 S N N 0 -0.181 1.657 0.607
9 C11 C C9 S N N 0 -0.71 -1.777 -0.746
10 C19 C C10 N N N 0 -3.894 1.817 0.912
11 C27 C C11 N N N 0 5.181 0.214 0.139
12 N01 N N1 N N N 0 3.482 -1.813 -2.302
13 N03 N N2 N N N 0 4.922 -0.762 -0.76
14 N04 N N3 N N N 0 2.772 0.072 -1.16
15 N06 N N4 N Y N 0 2.181 2.104 0.158
16 N25 N N5 N Y N 0 4.085 2.252 1.212
17 O09 O O1 N N N 0 -0.043 0.252 0.386
18 O12 O O2 N N N 0 0.626 -2.057 -1.168
19 O14 O O3 N N N 0 -0.676 -4.123 0.793
20 O15 O O4 N N N 0 -0.139 -1.916 1.894
21 O16 O O5 N N N 0 -2.552 -2.349 1.292
22 O18 O O6 N N N 0 -2.527 1.475 1.155
23 O21 O O7 N N N 0 -3.67 1.306 -1.734
24 O22 O O8 N N N 0 -4.369 -0.661 -0.315
25 O23 O O9 N N N 0 -6.029 1.31 -0.837
26 O28 O O10 N N N 0 6.256 0.268 0.71
27 P13 P P1 N N N 0 -1.009 -2.55 0.878
28 P20 P P2 N N N 0 -4.49 0.925 -0.562
29 H1 H H1 N N N 0 -0.658 0.206 -1.586
30 H2 H H2 N N N 0 -1.94 -0.047 -0.378
31 H3 H H3 N N N 0 -1.685 3.175 0.338
32 H4 H H4 N N N 0 -1.835 1.788 -0.766
33 H5 H H5 N N N 0 2.574 3.68 1.603
34 H6 H H6 N N N 0 0.686 2.106 -1.313
35 H7 H H7 N N N 0 0.64 3.484 -0.187
36 H8 H H8 N N N 0 0.019 1.881 1.655
37 H9 H H9 N N N 0 -1.413 -2.179 -1.475
38 H10 H H10 N N N 0 -4.497 1.537 1.775
39 H11 H H11 N N N 0 -3.975 2.891 0.744
40 H12 H H12 N N N 0 2.629 -1.862 -2.762
41 H13 H H13 N N N 0 4.169 -2.473 -2.485
42 H14 H H14 N N N 0 5.598 -1.429 -0.956
43 H15 H H15 N N N 0 1.306 -1.727 -0.565
44 H16 H H16 N N N 0 -0.813 -4.599 1.623
45 H17 H H17 N N N 0 -3.18 -2.74 0.669
46 H18 H H18 N N N 0 -4.882 -0.982 0.439
47 H19 H H19 N N N 0 -6.412 0.871 -1.608



8QI : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O28 C27 O C doub 1.22 N N
2 N03 C27 N C sing 1.35 N N
3 N03 C02 N C sing 1.36 N N
4 N01 C02 N C sing 1.37 N N
5 C27 C26 C C sing 1.41 N N
6 C02 N04 C N doub 1.31 N N
7 C26 C05 C C doub 1.4 N Y
8 C26 N25 C N sing 1.35 N Y
9 N04 C05 N C sing 1.34 N N
10 C05 N06 C N sing 1.37 N Y
11 N25 C24 N C doub 1.3 N Y
12 N06 C24 N C sing 1.37 N Y
13 N06 C07 N C sing 1.46 N N
14 O15 P13 O P doub 1.48 N N
15 O14 P13 O P sing 1.61 N N
16 P13 O16 P O sing 1.61 N N
17 P13 C11 P C sing 1.82 N N
18 C07 C08 C C sing 1.53 N N
19 C10 C11 C C sing 1.53 N N
20 C10 O09 C O sing 1.43 N N
21 C08 O09 C O sing 1.43 N N
22 C08 C17 C C sing 1.53 N N
23 C11 O12 C O sing 1.43 N N
24 C19 O18 C O sing 1.43 N N
25 C19 P20 C P sing 1.82 N N
26 C17 O18 C O sing 1.43 N N
27 O21 P20 O P doub 1.48 N N
28 P20 O23 P O sing 1.61 N N
29 P20 O22 P O sing 1.61 N N
30 C10 H1 C H sing 1.09 N N
31 C10 H2 C H sing 1.09 N N
32 C17 H3 C H sing 1.09 N N
33 C17 H4 C H sing 1.09 N N
34 C24 H5 C H sing 1.08 N N
35 C07 H6 C H sing 1.09 N N
36 C07 H7 C H sing 1.09 N N
37 C08 H8 C H sing 1.09 N N
38 C11 H9 C H sing 1.09 N N
39 C19 H10 C H sing 1.09 N N
40 C19 H11 C H sing 1.09 N N
41 N01 H12 N H sing 0.97 N N
42 N01 H13 N H sing 0.97 N N
43 N03 H14 N H sing 0.97 N N
44 O12 H15 O H sing 0.97 N N
45 O14 H16 O H sing 0.97 N N
46 O16 H17 O H sing 0.97 N N
47 O22 H18 O H sing 0.97 N N
48 O23 H19 O H sing 0.97 N N



8QI : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
8QI 7san Open in New Window Bound ligand 4 1
8QI 7sb7 Open in New Window Bound ligand 2 1
8QI 7scr Open in New Window Bound ligand 6 1