Chemical Components in the PDB

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K2R : Summary

Code

K2R

One-letter code

X

Molecule name

3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 3-[3-[9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid

Formula

C19 H21 N4 O9 P

Formal charge

0

Molecular weight

480.365 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c2ncnc3c4cccc(CCC(O)=O)c4
SMILES OpenEye OEToolkits 2.0.7 c1cc(cc(c1)c2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(O)O)O)O)CCC(=O)O
Canonical SMILES CACTVS 3.385 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c2ncnc3c4cccc(CCC(O)=O)c4
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(cc(c1)c2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)CCC(=O)O

IUPAC InChI

InChI=1S/C19H21N4O9P/c24-13(25)5-4-10-2-1-3-11(6-10)14-15-18(21-8-20-14)23(9-22-15)19-17(27)16(26)12(32-19)7-31-33(28,29)30/h1-3,6,8-9,12,16-17,19,26-27H,4-5,7H2,(H,24,25)(H2,28,29,30)/t12-,16-,17-,19-/m1/s1

IUPAC InChI key

OPBOIJBNPKQEFR-MYFFOXHASA-N
K2R

wwPDB Information

Atom count

54 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-05-25

Last modified at

2020-11-20

Status

Released

Obsoleted

Not Assigned



K2R : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OZ1 O O1 N N N 0 -9.393 -0.243 -2.758
2 CZ C C1 N N N 0 -8.976 0.034 -1.513
3 OZ2 O O2 N N N 0 -9.738 -0.083 -0.581
4 CE C C2 N N N 0 -7.56 0.489 -1.275
5 CD2 C C3 N N N 0 -7.346 0.734 0.22
6 CG1 C C4 N Y N 0 -5.93 1.189 0.457
7 CB1 C C5 N Y N 0 -4.939 0.259 0.698
8 CD1 C C6 N Y N 0 -5.624 2.538 0.428
9 CG2 C C7 N Y N 0 -4.326 2.963 0.645
10 CB2 C C8 N Y N 0 -3.327 2.043 0.892
11 CA C C9 N Y N 0 -3.627 0.682 0.911
12 C6 C C10 N Y N 0 -2.56 -0.311 1.176
13 N1 N N1 N Y N 0 -2.819 -1.424 1.859
14 C2 C C11 N Y N 0 -1.874 -2.313 2.099
15 N3 N N2 N Y N 0 -0.633 -2.158 1.686
16 C4 C C12 N Y N 0 -0.279 -1.081 0.998
17 C5 C C13 N Y N 0 -1.25 -0.103 0.708
18 N7 N N3 N Y N 0 -0.633 0.876 0.007
19 C8 C C14 N Y N 0 0.623 0.572 -0.15
20 N9 N N4 N Y N 0 0.89 -0.628 0.439
21 C1' C C15 R N N 0 2.187 -1.308 0.472
22 C2' C C16 R N N 0 2.318 -2.273 -0.727
23 O2' O O3 N N N 0 2.011 -3.611 -0.329
24 O4' O O4 N N N 0 3.259 -0.355 0.297
25 C4' C C17 R N N 0 4.392 -1.134 -0.146
26 C3' C C18 S N N 0 3.802 -2.156 -1.143
27 O3' O O5 N N N 0 4.459 -3.418 -1.013
28 C5' C C19 N N N 0 5.414 -0.236 -0.846
29 O5' O O6 N N N 0 5.978 0.672 0.101
30 P P P1 N N N 0 7.092 1.767 -0.289
31 O3P O O7 N N N 0 7.4 2.698 0.988
32 O2P O O8 N N N 0 8.443 1.018 -0.745
33 O1P O O9 N N N 0 6.592 2.605 -1.402
34 H1 H H1 N N N 0 -10.31 -0.531 -2.861
35 H5 H H5 N N N 0 -7.528 -0.19 0.769
36 H2 H H2 N N N 0 -6.868 -0.281 -1.62
37 H3 H H3 N N N 0 -7.378 1.413 -1.824
38 H4 H H4 N N N 0 -8.038 1.503 0.564
39 H6 H H6 N N N 0 -5.179 -0.794 0.721
40 H7 H H7 N N N 0 -6.402 3.262 0.235
41 H8 H H8 N N N 0 -4.093 4.018 0.621
42 H9 H H9 N N N 0 -2.314 2.377 1.061
43 H10 H H10 N N N 0 -2.128 -3.203 2.657
44 H11 H H11 N N N 0 1.346 1.179 -0.674
45 H12 H H12 N N N 0 2.309 -1.848 1.411
46 H13 H H13 N N N 0 1.667 -1.96 -1.543
47 H14 H H14 N N N 0 2.078 -4.259 -1.043
48 H15 H H15 N N N 0 4.853 -1.647 0.697
49 H16 H H16 N N N 0 3.884 -1.785 -2.164
50 H17 H H17 N N N 0 4.089 -4.114 -1.574
51 H18 H H18 N N N 0 6.205 -0.852 -1.275
52 H19 H H19 N N N 0 4.921 0.326 -1.64
53 H20 H H20 N N N 0 8.064 3.382 0.825
54 H21 H H21 N N N 0 8.827 0.45 -0.064



K2R : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3' C3' O C sing 1.43 N N
2 O2' C2' O C sing 1.43 N N
3 C3' C2' C C sing 1.55 N N
4 C3' C4' C C sing 1.54 N N
5 C2' C1' C C sing 1.54 N N
6 C4' C5' C C sing 1.53 N N
7 C4' O4' C O sing 1.44 N N
8 C5' O5' C O sing 1.43 N N
9 O1P P O P doub 1.48 N N
10 O5' P O P sing 1.61 N N
11 C1' O4' C O sing 1.44 N N
12 C1' N9 C N sing 1.46 N N
13 O3P P O P sing 1.61 N N
14 P O2P P O sing 1.61 N N
15 N9 C4 N C sing 1.37 N Y
16 N9 C8 N C sing 1.36 N Y
17 N3 C4 N C sing 1.33 N Y
18 N3 C2 N C doub 1.32 N Y
19 C4 C5 C C doub 1.41 N Y
20 C2 N1 C N sing 1.32 N Y
21 C8 N7 C N doub 1.3 N Y
22 C5 N7 C N sing 1.35 N Y
23 C5 C6 C C sing 1.41 N Y
24 N1 C6 N C doub 1.33 N Y
25 C6 CA C C sing 1.48 N N
26 CA CB2 C C doub 1.39 N Y
27 CA CB1 C C sing 1.39 N Y
28 CB2 CG2 C C sing 1.38 N Y
29 CB1 CG1 C C doub 1.38 N Y
30 CG2 CD1 C C doub 1.38 N Y
31 CG1 CD1 C C sing 1.38 N Y
32 CG1 CD2 C C sing 1.51 N N
33 CE CD2 C C sing 1.53 N N
34 CE CZ C C sing 1.51 N N
35 OZ2 CZ O C doub 1.21 N N
36 CZ OZ1 C O sing 1.34 N N
37 OZ1 H1 O H sing 0.97 N N
38 CE H2 C H sing 1.09 N N
39 CE H3 C H sing 1.09 N N
40 CD2 H4 C H sing 1.09 N N
41 CD2 H5 C H sing 1.09 N N
42 CB1 H6 C H sing 1.08 N N
43 CD1 H7 C H sing 1.08 N N
44 CG2 H8 C H sing 1.08 N N
45 CB2 H9 C H sing 1.08 N N
46 C2 H10 C H sing 1.08 N N
47 C8 H11 C H sing 1.08 N N
48 C1' H12 C H sing 1.09 N N
49 C2' H13 C H sing 1.09 N N
50 O2' H14 O H sing 0.97 N N
51 C4' H15 C H sing 1.09 N N
52 C3' H16 C H sing 1.09 N N
53 O3' H17 O H sing 0.97 N N
54 C5' H18 C H sing 1.09 N N
55 C5' H19 C H sing 1.09 N N
56 O3P H20 O H sing 0.97 N N
57 O2P H21 O H sing 0.97 N N



K2R : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
K2R 7c6b Open in New Window Bound ligand 3 1