Chemical Components in the PDB

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OKR : Summary

Code

OKR

One-letter code

X

Molecule name

[[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Formula

C20 H28 N10 O21 P4

Formal charge

0

Molecular weight

868.386 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[CH]4[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]4n5cnc6C(=O)NC(=Nc56)N)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.7 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5N=C(NC6=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[C@@H]4[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]4n5cnc6C(=O)NC(=Nc56)N)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5N=C(NC6=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C20H28N10O21P4/c21-19-25-13-7(15(34)27-19)23-3-29(13)17-11(33)9(31)5(47-17)1-45-53(39,40)49-12-10(32)6(2-46-54(41,42)51-55(43,44)50-52(36,37)38)48-18(12)30-4-24-8-14(30)26-20(22)28-16(8)35/h3-6,9-12,17-18,31-33H,1-2H2,(H,39,40)(H,41,42)(H,43,44)(H2,36,37,38)(H3,21,25,27,34)(H3,22,26,28,35)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1

IUPAC InChI key

GILDQNNERNWCKN-MHARETSRSA-N
OKR

wwPDB Information

Atom count

83 (55 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-05-10

Last modified at

2023-05-05

Status

Released

Obsoleted

Not Assigned



OKR : Atoms of Molecule

Total Number of Atoms: 83
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -10.502 5.147 -0.35
2 C1 C C1 N N N 0 -9.941 4.053 -0.96
3 N2 N N2 N N N 0 -9.093 3.31 -0.285
4 C2 C C2 N Y N 0 -8.521 2.235 -0.84
5 C3 C C3 N Y N 0 -8.83 1.89 -2.16
6 N3 N N3 N Y N 0 -8.12 0.775 -2.461
7 C4 C C4 N Y N 0 -7.411 0.424 -1.427
8 N4 N N4 N Y N 0 -7.627 1.297 -0.401
9 C5 C C5 R N N 0 -7.013 1.24 0.928
10 O1 O O1 N N N 0 -5.787 0.478 0.884
11 C6 C C6 R N N 0 -5.544 0.068 2.247
12 C7 C C7 N N N 0 -4.601 -1.136 2.279
13 O2 O O2 N N N 0 -3.292 -0.727 1.878
14 P1 P P1 N N N 0 -2.043 -1.74 1.796
15 O3 O O3 N N N 0 -1.871 -2.418 3.1
16 O4 O O4 N N N 0 -2.317 -2.838 0.651
17 O5 O O5 N N N 0 -0.706 -0.916 1.439
18 C8 C C8 R N N 0 0.59 -1.516 1.397
19 C9 C C9 R N N 0 1.569 -0.756 2.32
20 O6 O O6 N N N 0 0.907 0.337 2.96
21 C10 C C10 R N N 0 2.664 -0.239 1.361
22 C11 C C11 N N N 0 4.036 -0.306 2.034
23 O7 O O7 N N N 0 5.016 0.282 1.177
24 P2 P P2 N N N 0 6.575 0.384 1.567
25 O8 O O8 N N N 0 7.089 -0.964 1.9
26 O9 O O9 N N N 0 6.748 1.354 2.84
27 O12 O O12 N N N 0 9.798 1.148 1.098
28 O10 O O10 N N N 0 7.402 0.981 0.321
29 P3 P P3 N N N 0 8.955 0.959 -0.104
30 O11 O O11 N N N 0 9.304 -0.457 -0.787
31 O15 O O15 N N N 0 10.227 3.706 -3.025
32 O13 O O13 N N N 0 9.242 2.146 -1.152
33 P4 P P4 N N N 0 10.579 2.848 -1.709
34 O14 O O14 N N N 0 11.576 1.809 -2.051
35 O16 O O16 N N N 0 11.185 3.822 -0.58
36 O17 O O17 N N N 0 2.615 -1.133 0.228
37 C12 C C12 R N N 0 1.21 -1.369 -0.01
38 N5 N N5 N Y N 0 1.022 -2.6 -0.781
39 C13 C C13 N Y N 0 1.919 -3.622 -0.9
40 N6 N N6 N Y N 0 1.425 -4.556 -1.66
41 C14 C C14 N Y N 0 0.186 -4.191 -2.072
42 C15 C C15 N N N 0 -0.799 -4.795 -2.888
43 O18 O O18 N N N 0 -0.604 -5.885 -3.398
44 N7 N N7 N N N 0 -1.96 -4.135 -3.087
45 C16 C C16 N N N 0 -2.167 -2.916 -2.511
46 N8 N N8 N N N 0 -3.357 -2.269 -2.731
47 N9 N N9 N N N 0 -1.26 -2.344 -1.752
48 C17 C C17 N Y N 0 -0.086 -2.938 -1.509
49 C18 C C18 S N N 0 -6.934 -0.323 2.795
50 O19 O O19 N N N 0 -7.062 0.073 4.162
51 C19 C C19 R N N 0 -7.924 0.468 1.909
52 O20 O O20 N N N 0 -8.693 1.375 2.702
53 C20 C C20 N N N 0 -9.744 2.697 -2.876
54 O21 O O21 N N N 0 -10.042 2.434 -4.028
55 N10 N N10 N N N 0 -10.285 3.765 -2.247
56 H1 H H1 N N N 0 -11.133 5.702 -0.834
57 H2 H H2 N N N 0 -10.27 5.362 0.567
58 H3 H H3 N N N 0 -6.752 -0.431 -1.388
59 H4 H H4 N N N 0 -6.822 2.246 1.301
60 H5 H H5 N N N 0 -5.126 0.893 2.824
61 H6 H H6 N N N 0 -4.561 -1.541 3.29
62 H7 H H7 N N N 0 -4.967 -1.902 1.595
63 H8 H H8 N N N 0 -2.44 -2.464 -0.232
64 H9 H H9 N N N 0 0.533 -2.567 1.681
65 H10 H H10 N N N 0 1.997 -1.43 3.061
66 H11 H H11 N N N 0 1.475 0.85 3.551
67 H12 H H12 N N N 0 2.444 0.783 1.05
68 H13 H H13 N N N 0 4.005 0.237 2.978
69 H14 H H14 N N N 0 4.297 -1.348 2.223
70 H15 H H15 N N N 0 6.431 2.256 2.694
71 H16 H H16 N N N 0 8.788 -0.647 -1.582
72 H17 H H17 N N N 0 10.988 4.158 -3.416
73 H18 H H18 N N N 0 10.584 4.529 -0.307
74 H19 H H19 N N N 0 0.766 -0.521 -0.533
75 H20 H H20 N N N 0 2.893 -3.651 -0.435
76 H21 H H21 N N N 0 -2.651 -4.529 -3.643
77 H22 H H22 N N N 0 -4.036 -2.679 -3.29
78 H23 H H23 N N N 0 -3.519 -1.401 -2.329
79 H24 H H24 N N N 0 -7.098 -1.395 2.691
80 H25 H H25 N N N 0 -7.917 -0.148 4.557
81 H26 H H26 N N N 0 -8.578 -0.213 1.365
82 H27 H H27 N N N 0 -9.237 0.944 3.375
83 H28 H H28 N N N 0 -10.918 4.331 -2.716



OKR : Chemical Bonds

Total Number of Bonds: 88
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O19 C18 O C sing 1.43 N N
2 C7 C6 C C sing 1.53 N N
3 C7 O2 C O sing 1.43 N N
4 C6 C18 C C sing 1.54 N N
5 C6 O1 C O sing 1.44 N N
6 O2 P1 O P sing 1.61 N N
7 C18 C19 C C sing 1.55 N N
8 O1 C5 O C sing 1.44 N N
9 O6 C9 O C sing 1.43 N N
10 O3 P1 O P doub 1.48 N N
11 N8 C16 N C sing 1.37 N N
12 O8 P2 O P doub 1.48 N N
13 O9 P2 O P sing 1.61 N N
14 N7 C16 N C sing 1.36 N N
15 N7 C15 N C sing 1.35 N N
16 P1 O5 P O sing 1.61 N N
17 P1 O4 P O sing 1.61 N N
18 C16 N9 C N doub 1.31 N N
19 C19 C5 C C sing 1.55 N N
20 C19 O20 C O sing 1.43 N N
21 O18 C15 O C doub 1.22 N N
22 C5 N4 C N sing 1.47 N N
23 C9 C8 C C sing 1.55 N N
24 C9 C10 C C sing 1.54 N N
25 C15 C14 C C sing 1.41 N N
26 C8 O5 C O sing 1.43 N N
27 C8 C12 C C sing 1.54 N N
28 P2 O7 P O sing 1.61 N N
29 P2 O10 P O sing 1.61 N N
30 N9 C17 N C sing 1.34 N N
31 C14 C17 C C doub 1.4 N Y
32 C14 N6 C N sing 1.36 N Y
33 C17 N5 C N sing 1.37 N Y
34 O7 C11 O C sing 1.43 N N
35 N6 C13 N C doub 1.3 N Y
36 N2 C1 N C doub 1.31 N N
37 N2 C2 N C sing 1.34 N N
38 N1 C1 N C sing 1.37 N N
39 N5 C13 N C sing 1.37 N Y
40 N5 C12 N C sing 1.46 N N
41 O12 P3 O P doub 1.48 N N
42 N4 C2 N C sing 1.37 N Y
43 N4 C4 N C sing 1.36 N Y
44 C12 O17 C O sing 1.44 N N
45 C10 C11 C C sing 1.53 N N
46 C10 O17 C O sing 1.44 N N
47 C1 N10 C N sing 1.36 N N
48 O10 P3 O P sing 1.61 N N
49 C2 C3 C C doub 1.4 N Y
50 O14 P4 O P doub 1.48 N N
51 P3 O11 P O sing 1.61 N N
52 P3 O13 P O sing 1.61 N N
53 C4 N3 C N doub 1.3 N Y
54 N10 C20 N C sing 1.35 N N
55 C3 N3 C N sing 1.36 N Y
56 C3 C20 C C sing 1.41 N N
57 P4 O13 P O sing 1.61 N N
58 P4 O16 P O sing 1.61 N N
59 P4 O15 P O sing 1.61 N N
60 C20 O21 C O doub 1.22 N N
61 N1 H1 N H sing 0.97 N N
62 N1 H2 N H sing 0.97 N N
63 C4 H3 C H sing 1.08 N N
64 C5 H4 C H sing 1.09 N N
65 C6 H5 C H sing 1.09 N N
66 C7 H6 C H sing 1.09 N N
67 C7 H7 C H sing 1.09 N N
68 O4 H8 O H sing 0.97 N N
69 C8 H9 C H sing 1.09 N N
70 C9 H10 C H sing 1.09 N N
71 O6 H11 O H sing 0.97 N N
72 C10 H12 C H sing 1.09 N N
73 C11 H13 C H sing 1.09 N N
74 C11 H14 C H sing 1.09 N N
75 O9 H15 O H sing 0.97 N N
76 O11 H16 O H sing 0.97 N N
77 O15 H17 O H sing 0.97 N N
78 O16 H18 O H sing 0.97 N N
79 C12 H19 C H sing 1.09 N N
80 C13 H20 C H sing 1.08 N N
81 N7 H21 N H sing 0.97 N N
82 N8 H22 N H sing 0.97 N N
83 N8 H23 N H sing 0.97 N N
84 C18 H24 C H sing 1.09 N N
85 O19 H25 O H sing 0.97 N N
86 C19 H26 C H sing 1.09 N N
87 O20 H27 O H sing 0.97 N N
88 N10 H28 N H sing 0.97 N N



OKR : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
OKR 7uzr Open in New Window Bound ligand 2 1
OKR 7v0c Open in New Window Bound ligand 2 1
OKR 8sj8 Open in New Window Bound ligand 1 1