Chemical Components in the PDB

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K2K : Summary

Code

K2K

One-letter code

X

Molecule name

(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-(6-azanyl-9~{H}-purin-8-yl)but-3-ynylamino]methyl]oxolane-3,4-diol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-(6-azanyl-9~{H}-purin-8-yl)but-3-ynylamino]methyl]oxolane-3,4-diol

Formula

C19 H21 N11 O3

Formal charge

0

Molecular weight

451.442 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CNCCC#Cc4[nH]c5ncnc(N)c5n4)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)[nH]c(n2)C#CCCNCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CNCCC#Cc4[nH]c5ncnc(N)c5n4)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)[nH]c(n2)C#CCCNC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N

IUPAC InChI

InChI=1S/C19H21N11O3/c20-15-11-17(25-6-23-15)29-10(28-11)3-1-2-4-22-5-9-13(31)14(32)19(33-9)30-8-27-12-16(21)24-7-26-18(12)30/h6-9,13-14,19,22,31-32H,2,4-5H2,(H2,21,24,26)(H3,20,23,25,28,29)/t9-,13-,14-,19-/m1/s1

IUPAC InChI key

ZVZLLIKFDIWTQZ-NBKUUXFISA-N
K2K

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

2019-04-16

Last modified at

2020-02-14

Status

Released

Obsoleted

Not Assigned



K2K : 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 C2 C C1 N Y N 0 8.461 -0.497 0.825
2 C4 C C2 N Y N 0 6.27 -0.615 0.141
3 C5 C C3 N Y N 0 6.535 -1.859 -0.457
4 C6 C C4 N Y N 0 7.837 -2.379 -0.357
5 N9 N N1 N Y N 0 4.943 -0.357 -0.094
6 C8 C C5 N Y N 0 4.443 -1.407 -0.805
7 CAK C C6 R N N 0 4.201 0.829 0.339
8 CAN C C9 R N N 0 2.131 1.823 0.351
9 CAL C C7 R N N 0 4.316 1.951 -0.717
10 CAM C C8 S N N 0 2.923 2.619 -0.709
11 CAP C C10 N N N 0 0.675 1.655 -0.087
12 CAR C C11 N N N 0 -1.493 0.823 0.6
13 CAS C C12 N N N 0 -2.253 0.141 1.739
14 CAT C C13 N N N 0 -3.662 -0.038 1.352
15 CAU C C14 N N N 0 -4.785 -0.18 1.044
16 CAV C C15 N Y N 0 -6.156 -0.354 0.667
17 CAX C C16 N Y N 0 -8.295 -0.909 0.734
18 CAZ C C17 N Y N 0 -10.478 -1.151 0.055
19 CBB C C18 N Y N 0 -9.031 -0.141 -1.432
20 CBC C C19 N Y N 0 -7.993 -0.296 -0.495
21 N1 N N2 N Y N 0 8.757 -1.664 0.283
22 N3 N N3 N Y N 0 7.254 0.024 0.766
23 N6 N N4 N N N 0 8.157 -3.599 -0.926
24 N7 N N5 N Y N 0 5.378 -2.287 -1.016
25 NAQ N N6 N N N 0 -0.087 1.001 0.986
26 NAW N N7 N Y N 0 -7.124 -0.932 1.45
27 NAY N N8 N Y N 0 -9.54 -1.315 0.964
28 NBA N N9 N Y N 0 -10.243 -0.585 -1.114
29 NBD N N10 N Y N 0 -6.68 0.021 -0.477
30 NBE N N11 N N N 0 -8.794 0.451 -2.66
31 OAO O O1 N N N 0 2.788 0.538 0.415
32 OBF O O2 N N N 0 3.029 3.993 -0.327
33 OBG O O3 N N N 0 5.325 2.891 -0.342
34 H1 H H1 N N N 0 9.238 0.048 1.34
35 H2 H H2 N N N 0 3.421 -1.496 -1.142
36 H3 H H3 N N N 0 4.569 1.176 1.304
37 H4 H H4 N N N 0 4.534 1.53 -1.699
38 H5 H H5 N N N 0 2.45 2.529 -1.687
39 H6 H H6 N N N 0 2.182 2.323 1.318
40 H7 H H7 N N N 0 0.243 2.634 -0.295
41 H8 H H8 N N N 0 0.635 1.041 -0.987
42 H9 H H9 N N N 0 -1.548 0.204 -0.296
43 H10 H H10 N N N 0 -1.94 1.796 0.396
44 H11 H H11 N N N 0 -1.806 -0.832 1.942
45 H12 H H12 N N N 0 -2.197 0.76 2.635
46 H16 H H16 N N N 0 0.332 0.12 1.242
47 H13 H H13 N N N 0 -11.479 -1.493 0.275
48 H14 H H14 N N N 0 7.479 -4.106 -1.4
49 H15 H H15 N N N 0 9.059 -3.947 -0.85
50 H18 H H18 N N N 0 -7.003 -1.291 2.343
51 H20 H H20 N N N 0 -9.517 0.546 -3.301
52 H21 H H21 N N N 0 -7.905 0.771 -2.881
53 H22 H H22 N N N 0 3.568 4.527 -0.927
54 H23 H H23 N N N 0 5.44 3.617 -0.97



K2K : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N6 C6 N C sing 1.38 N N
2 N7 C8 N C doub 1.3 N Y
3 N7 C5 N C sing 1.35 N Y
4 C6 C5 C C doub 1.41 N Y
5 C6 N1 C N sing 1.33 N Y
6 OBF CAM O C sing 1.43 N N
7 C8 N9 C N sing 1.36 N Y
8 C5 C4 C C sing 1.41 N Y
9 CAM CAL C C sing 1.54 N N
10 CAM CAN C C sing 1.54 N N
11 CAL OBG C O sing 1.43 N N
12 CAL CAK C C sing 1.55 N N
13 N1 C2 N C doub 1.32 N Y
14 N9 C4 N C sing 1.37 N Y
15 N9 CAK N C sing 1.46 N N
16 C4 N3 C N doub 1.33 N Y
17 C2 N3 C N sing 1.32 N Y
18 CAK OAO C O sing 1.44 N N
19 CAN OAO C O sing 1.44 N N
20 CAN CAP C C sing 1.53 N N
21 CAP NAQ C N sing 1.47 N N
22 NBE CBB N C sing 1.38 N N
23 NAQ CAR N C sing 1.47 N N
24 CBB NBA C N doub 1.33 N Y
25 CBB CBC C C sing 1.41 N Y
26 NBA CAZ N C sing 1.32 N Y
27 NBD CBC N C sing 1.35 N Y
28 NBD CAV N C doub 1.31 N Y
29 CBC CAX C C doub 1.41 N Y
30 CAR CAS C C sing 1.53 N N
31 CAZ NAY C N doub 1.32 N Y
32 CAV CAU C C sing 1.43 N N
33 CAV NAW C N sing 1.37 N Y
34 CAX NAY C N sing 1.33 N Y
35 CAX NAW C N sing 1.37 N Y
36 CAU CAT C C trip 1.17 N N
37 CAT CAS C C sing 1.47 N N
38 C2 H1 C H sing 1.08 N N
39 C8 H2 C H sing 1.08 N N
40 CAK H3 C H sing 1.09 N N
41 CAL H4 C H sing 1.09 N N
42 CAM H5 C H sing 1.09 N N
43 CAN H6 C H sing 1.09 N N
44 CAP H7 C H sing 1.09 N N
45 CAP H8 C H sing 1.09 N N
46 CAR H9 C H sing 1.09 N N
47 CAR H10 C H sing 1.09 N N
48 CAS H11 C H sing 1.09 N N
49 CAS H12 C H sing 1.09 N N
50 CAZ H13 C H sing 1.08 N N
51 N6 H14 N H sing 0.97 N N
52 N6 H15 N H sing 0.97 N N
53 NAQ H16 N H sing 1.01 N N
54 NAW H18 N H sing 0.97 N N
55 NBE H20 N H sing 0.97 N N
56 NBE H21 N H sing 0.97 N N
57 OBF H22 O H sing 0.97 N N
58 OBG H23 O H sing 0.97 N N



K2K : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
K2K 6rg8 Open in New Window Bound ligand 1 1