Chemical Components in the PDB

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BLK : Summary

Code

BLK

One-letter code

X

Molecule name

[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-O-[(R)-({(2S)-2-amino-6-[(tert-butoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine
OpenEye OEToolkits 1.7.6 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate

Formula

C21 H34 N7 O10 P

Formal charge

0

Molecular weight

575.509 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OC(C)(C)C)NCCCCC(N)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.370 CC(C)(C)OC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.7.6 CC(C)(C)OC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
Canonical SMILES CACTVS 3.370 CC(C)(C)OC(=O)NCCCC[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)(C)OC(=O)NCCCC[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N

IUPAC InChI

InChI=1S/C21H34N7O10P/c1-21(2,3)37-20(32)24-7-5-4-6-11(22)19(31)38-39(33,34)35-8-12-14(29)15(30)18(36-12)28-10-27-13-16(23)25-9-26-17(13)28/h9-12,14-15,18,29-30H,4-8,22H2,1-3H3,(H,24,32)(H,33,34)(H2,23,25,26)/t11-,12+,14+,15+,18+/m0/s1

IUPAC InChI key

XYDQQGDGPLGSGU-URQYDQELSA-N
BLK

wwPDB Information

Atom count

73 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-05-01

Last modified at

2012-12-28

Status

Released

Obsoleted

Not Assigned



BLK : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 1.598 -3.645 -0.314
2 C1' C C1' R N N 0 -5.27 0.295 0.763
3 C2 C C2 N Y N 0 -7.681 4.068 1.071
4 C2' C C2' R N N 0 -6.347 -0.687 0.226
5 C3' C C3' S N N 0 -5.777 -2.06 0.657
6 C4 C C4 N Y N 0 -6.106 2.623 0.227
7 C4' C C4' R N N 0 -4.276 -1.793 0.878
8 C5 C C5 N Y N 0 -5.762 3.581 -0.742
9 C5' C C5' N N N 0 -3.447 -2.7 -0.034
10 C6 C C6 N Y N 0 -6.454 4.804 -0.74
11 C8 C C8 N Y N 0 -4.495 1.852 -1.066
12 CA C CA S N N 0 2.964 -3.374 0.263
13 CB C CB N N N 0 3.537 -2.1 -0.36
14 CD C CD N N N 0 5.44 -0.482 -0.309
15 CE C CE N N N 0 6.769 -0.138 0.366
16 CG C CG N N N 0 4.866 -1.756 0.315
17 CT C CT N N N 0 10.265 3.176 0.183
18 CT1 C CT1 N N N 0 11.336 2.102 -0.018
19 CT2 C CT2 N N N 0 10.12 3.477 1.676
20 CT3 C CT3 N N N 0 10.675 4.45 -0.557
21 CZ C CZ N N N 0 8.492 1.578 0.209
22 H1 H H1 N N N 0 12.288 2.459 0.374
23 H10 H H10 N N N 0 6.838 1.533 -0.942
24 H11 H H11 N N N 0 7.472 -0.96 0.225
25 H12 H H12 N N N 0 6.606 0.021 1.432
26 H13 H H13 N N N 0 4.738 0.34 -0.167
27 H14 H H14 N N N 0 5.604 -0.641 -1.375
28 H15 H H15 N N N 0 5.569 -2.578 0.173
29 H16 H H16 N N N 0 4.703 -1.597 1.38
30 H17 H H17 N N N 0 2.835 -1.279 -0.219
31 H18 H H18 N N N 0 3.701 -2.259 -1.426
32 H19 H H19 N N N 0 2.883 -3.246 1.343
33 H2 H H2 N N N 0 11.043 1.194 0.509
34 H20 H H20 N N N 0 3.944 -4.645 -1.026
35 H21 H H21 N N N 0 4.756 -4.378 0.401
36 H23 H H23 N N N 0 -0.721 -1.944 -2.209
37 H24 H H24 N N N 0 -3.637 -2.44 -1.076
38 H25 H H25 N N N 0 -3.725 -3.74 0.137
39 H26 H H26 N N N 0 -4.016 -1.978 1.92
40 H27 H H27 N N N 0 -5.922 -2.8 -0.13
41 H28 H H28 N N N 0 -7.337 -2.68 1.79
42 H29 H H29 N N N 0 -6.427 -0.622 -0.859
43 H3 H H3 N N N 0 11.439 1.887 -1.082
44 H30 H H30 N N N 0 -8.296 -1.087 0.608
45 H31 H H31 N N N 0 -5.422 0.489 1.825
46 H32 H H32 N N N 0 -3.745 1.199 -1.487
47 H33 H H33 N N N 0 -8.454 4.267 1.799
48 H34 H H34 N N N 0 -6.64 6.628 -1.655
49 H35 H H35 N N N 0 -5.471 5.632 -2.337
50 H4 H H4 N N N 0 11.072 3.835 2.069
51 H5 H H5 N N N 0 9.357 4.243 1.82
52 H6 H H6 N N N 0 9.828 2.569 2.204
53 H7 H H7 N N N 0 10.779 4.235 -1.621
54 H8 H H8 N N N 0 9.913 5.215 -0.414
55 H9 H H9 N N N 0 11.627 4.808 -0.165
56 N N N N N N 0 3.853 -4.506 -0.031
57 N1 N N1 N Y N 0 -7.393 4.999 0.18
58 N3 N N3 N Y N 0 -7.062 2.907 1.105
59 N6 N N6 N N N 0 -6.159 5.786 -1.67
60 N7 N N7 N Y N 0 -4.775 3.046 -1.5
61 N9 N N9 N Y N 0 -5.286 1.546 0.0010
62 NZ N NZ N N N 0 7.319 1.082 -0.231
63 O O O N N N 0 1.465 -4.463 -1.193
64 O1 O O1 N N N 0 9.095 1.013 1.1
65 O1P O O1P N N N 0 -1.145 -4.779 -0.419
66 O2 O O2 N N N 0 8.997 2.699 -0.34
67 O2' O O2' N N N 0 -7.613 -0.444 0.843
68 O2P O O2P N N N 0 -0.88 -2.887 -2.068
69 O3' O O3' N N N 0 -6.391 -2.498 1.871
70 O3P O O3P N N N 0 0.529 -2.978 0.149
71 O4' O O4' N N N 0 -4.031 -0.415 0.55
72 O5' O O5' N N N 0 -2.058 -2.524 0.254
73 P P P N N N 0 -0.894 -3.324 -0.519



BLK : Chemical Bonds

Total Number of Bonds: 75
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 N1 C6 N C doub 1.33 N Y
3 N1 C2 N C sing 1.32 N Y
4 C6 C5 C C sing 1.41 N Y
5 C2 N3 C N doub 1.32 N Y
6 C5 N7 C N sing 1.35 N Y
7 C5 C4 C C doub 1.41 N Y
8 N7 C8 N C doub 1.3 N Y
9 N3 C4 N C sing 1.33 N Y
10 C4 N9 C N sing 1.37 N Y
11 C8 N9 C N sing 1.36 N Y
12 N9 C1' N C sing 1.46 N N
13 C1' C2' C C sing 1.55 N N
14 C1' O4' C O sing 1.44 N N
15 C2' C3' C C sing 1.55 N N
16 C2' O2' C O sing 1.43 N N
17 O4' C4' O C sing 1.44 N N
18 O1P P O P doub 1.48 N N
19 O2P P O P sing 1.61 N N
20 O5' P O P sing 1.61 N N
21 O5' C5' O C sing 1.43 N N
22 C3' C4' C C sing 1.54 N N
23 C3' O3' C O sing 1.43 N N
24 P O3P P O sing 1.61 N N
25 C4' C5' C C sing 1.53 N N
26 O C O C doub 1.21 N N
27 O3P C O C sing 1.34 N N
28 C CA C C sing 1.51 N N
29 CA N C N sing 1.47 N N
30 CA CB C C sing 1.53 N N
31 CB CG C C sing 1.53 N N
32 CG CD C C sing 1.53 N N
33 CD CE C C sing 1.53 N N
34 CE NZ C N sing 1.47 N N
35 CT2 CT C C sing 1.53 N N
36 CT1 CT C C sing 1.53 N N
37 O2 CZ O C sing 1.35 N N
38 O2 CT O C sing 1.45 N N
39 NZ CZ N C sing 1.35 N N
40 CZ O1 C O doub 1.22 N N
41 CT CT3 C C sing 1.53 N N
42 CT1 H1 C H sing 1.09 N N
43 CT1 H2 C H sing 1.09 N N
44 CT1 H3 C H sing 1.09 N N
45 CT2 H4 C H sing 1.09 N N
46 CT2 H5 C H sing 1.09 N N
47 CT2 H6 C H sing 1.09 N N
48 CT3 H7 C H sing 1.09 N N
49 CT3 H8 C H sing 1.09 N N
50 CT3 H9 C H sing 1.09 N N
51 NZ H10 N H sing 0.97 N N
52 CE H11 C H sing 1.09 N N
53 CE H12 C H sing 1.09 N N
54 CD H13 C H sing 1.09 N N
55 CD H14 C H sing 1.09 N N
56 CG H15 C H sing 1.09 N N
57 CG H16 C H sing 1.09 N N
58 CB H17 C H sing 1.09 N N
59 CB H18 C H sing 1.09 N N
60 CA H19 C H sing 1.09 N N
61 N H20 N H sing 1.01 N N
62 N H21 N H sing 1.01 N N
63 O2P H23 O H sing 0.97 N N
64 C5' H24 C H sing 1.09 N N
65 C5' H25 C H sing 1.09 N N
66 C4' H26 C H sing 1.09 N N
67 C3' H27 C H sing 1.09 N N
68 O3' H28 O H sing 0.97 N N
69 C2' H29 C H sing 1.09 N N
70 O2' H30 O H sing 0.97 N N
71 C1' H31 C H sing 1.09 N N
72 C8 H32 C H sing 1.08 N N
73 C2 H33 C H sing 1.08 N N
74 N6 H34 N H sing 0.97 N N
75 N6 H35 N H sing 0.97 N N



BLK : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BLK 3vqx Open in New Window Bound ligand 2 1