Chemical Components in the PDB

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YLB : Summary

Code

YLB

One-letter code

X

Molecule name

5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)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] (2R)-2-azanyl-6-(butanoylamino)hexanoate

Formula

C20 H32 N7 O9 P

Formal charge

0

Molecular weight

545.483 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCCCCC(N)C(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)CCC
SMILES CACTVS 3.385 CCCC(=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 CCCC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
Canonical SMILES CACTVS 3.385 CCCC(=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 CCCC(=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/C20H32N7O9P/c1-2-5-13(28)23-7-4-3-6-11(21)20(31)36-37(32,33)34-8-12-15(29)16(30)19(35-12)27-10-26-14-17(22)24-9-25-18(14)27/h9-12,15-16,19,29-30H,2-8,21H2,1H3,(H,23,28)(H,32,33)(H2,22,24,25)/p-1/t11-,12-,15-,16-,19-/m1/s1

IUPAC InChI key

OAECZBFMQNITMX-JCQVVMGJSA-M
YLB

wwPDB Information

Atom count

69 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-11-28

Last modified at

2014-03-14

Status

Released

Obsoleted

Not Assigned



YLB : Atoms of Molecule

Total Number of Atoms: 69
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 2.305 -2.116 -1.471
2 N N N N N N 0 4.099 -1.907 -3.096
3 O O O N N N 0 2.251 -3.283 -1.776
4 N1 N N1 N Y N 0 -8.586 3.462 -0.449
5 C2 C C2 N Y N 0 -8.237 3.129 0.78
6 C3 C C3 N N N 0 12.894 3.136 2.203
7 N3 N N3 N Y N 0 -7.238 2.311 1.034
8 C4 C C4 N Y N 0 -6.528 1.78 0.043
9 C5 C C5 N Y N 0 -6.86 2.103 -1.283
10 C6 C C6 N Y N 0 -7.935 2.98 -1.503
11 N6 N N6 N N N 0 -8.309 3.335 -2.788
12 N7 N N7 N Y N 0 -5.994 1.438 -2.085
13 C8 C C8 N Y N 0 -5.172 0.744 -1.352
14 N9 N N9 N Y N 0 -5.46 0.922 -0.032
15 CA C CA R N N 0 3.459 -1.267 -1.939
16 CB C CB N N N 0 4.478 -1.122 -0.807
17 C3' C C3' S N N 0 -4.338 -1.773 2.235
18 C1' C C1' R N N 0 -4.759 0.309 1.099
19 C2' C C2' R N N 0 -5.482 -0.984 1.554
20 O2' O O2' N N N 0 -6.522 -0.685 2.488
21 O3' O O3' N N N 0 -4.378 -1.59 3.652
22 C4' C C4' R N N 0 -3.053 -1.157 1.648
23 O4' O O4' N N N 0 -3.454 -0.159 0.695
24 C5' C C5' N N N 0 -2.228 -2.24 0.951
25 O5' O O5' N N N 0 -0.986 -1.685 0.512
26 OAD O OAD N N N 0 9.918 2.495 -0.65
27 OAF O OAF N N N 0 -0.47 -3.175 -1.459
28 OAI O OAI N N N 0 0.707 -3.686 0.715
29 CAM C CAM N N N 0 6.606 -0.016 -0.107
30 CAN C CAN N N N 0 5.587 -0.161 -1.239
31 CAO C CAO N N N 0 7.715 0.946 -0.539
32 NAW N NAW N N N 0 8.691 1.084 0.544
33 OAY O OAY N N N 0 1.335 -1.573 -0.718
34 CBA C CBA N N N 0 9.762 1.887 0.388
35 CBF C CBF N N N 0 11.875 2.991 1.071
36 CBK C CBK N N N 0 10.766 2.03 1.503
37 PBN P PBN N N N 0 0.133 -2.544 -0.264
38 HN H HN N N N 0 4.448 -2.823 -2.855
39 HNA H HNA N N N 0 3.465 -1.956 -3.879
40 H2 H H2 N N N 0 -8.793 3.543 1.609
41 H3 H H3 N N N 0 13.684 3.821 1.895
42 H3A H H3A N N N 0 12.398 3.529 3.091
43 H3B H H3B N N N 0 13.326 2.161 2.429
44 HN6 H HN6 N N N 0 -9.053 3.941 -2.927
45 HN6A H HN6A N N N 0 -7.826 2.977 -3.549
46 H8 H H8 N N N 0 -4.378 0.119 -1.734
47 HA H HA N N N 0 3.092 -0.282 -2.226
48 HB H HB N N N 0 3.982 -0.73 0.08
49 HBA H HBA N N N 0 4.91 -2.097 -0.581
50 H1' H H1' N N N 0 -4.677 1.015 1.926
51 H2' H H2' N N N 0 -5.877 -1.531 0.697
52 HO2' H HO2' N N N 0 -7.003 -1.463 2.802
53 H3' H H3' N N N 0 -4.403 -2.832 1.986
54 HO3' H HO3' N N N 0 -5.192 -1.908 4.066
55 H4' H H4' N N N 0 -2.466 -0.696 2.443
56 H5' H H5' N N N 0 -2.035 -3.055 1.648
57 H5'A H H5'A N N N 0 -2.78 -2.62 0.091
58 HAM H HAM N N N 0 6.11 0.377 0.78
59 HAMA H HAMA N N N 0 7.038 -0.991 0.119
60 HAN H HAN N N N 0 6.083 -0.553 -2.127
61 HANA H HANA N N N 0 5.155 0.814 -1.466
62 HAO H HAO N N N 0 8.211 0.553 -1.427
63 HAOA H HAOA N N N 0 7.283 1.92 -0.766
64 HNAW H HNAW N N N 0 8.566 0.598 1.375
65 HBF H HBF N N N 0 11.443 3.966 0.845
66 HBFA H HBFA N N N 0 12.371 2.599 0.183
67 HBK H HBK N N N 0 10.27 2.422 2.391
68 HBKA H HBKA N N N 0 11.198 1.055 1.729
69 HAI H HAI N N N 0 1.118 -3.343 1.521



YLB : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C O C O doub 1.21 N N
2 C CA C C sing 1.51 N N
3 C OAY C O sing 1.34 N N
4 N CA N C sing 1.47 N N
5 N1 C2 N C doub 1.32 N Y
6 N1 C6 N C sing 1.33 N Y
7 C2 N3 C N sing 1.32 N Y
8 C3 CBF C C sing 1.53 N N
9 N3 C4 N C doub 1.33 N Y
10 C4 C5 C C sing 1.4 N Y
11 C4 N9 C N sing 1.37 N Y
12 C5 C6 C C doub 1.4 N Y
13 C5 N7 C N sing 1.35 N Y
14 C6 N6 C N sing 1.38 N N
15 N7 C8 N C doub 1.3 N Y
16 C8 N9 C N sing 1.36 N Y
17 N9 C1' N C sing 1.47 N N
18 CA CB C C sing 1.53 N N
19 CB CAN C C sing 1.53 N N
20 C1' C2' C C sing 1.55 N N
21 C1' O4' C O sing 1.44 N N
22 C2' O2' C O sing 1.43 N N
23 C2' C3' C C sing 1.55 N N
24 C3' O3' C O sing 1.43 N N
25 C3' C4' C C sing 1.54 N N
26 C4' O4' C O sing 1.44 N N
27 C4' C5' C C sing 1.53 N N
28 C5' O5' C O sing 1.43 N N
29 O5' PBN O P sing 1.61 N N
30 OAD CBA O C doub 1.21 N N
31 OAF PBN O P doub 1.48 N N
32 OAI PBN O P sing 1.61 N N
33 CAM CAN C C sing 1.53 N N
34 CAM CAO C C sing 1.53 N N
35 CAO NAW C N sing 1.46 N N
36 NAW CBA N C sing 1.35 N N
37 OAY PBN O P sing 1.61 N N
38 CBA CBK C C sing 1.51 N N
39 CBF CBK C C sing 1.53 N N
40 N HN N H sing 1.01 N N
41 N HNA N H sing 1.01 N N
42 C2 H2 C H sing 1.08 N N
43 C3 H3 C H sing 1.09 N N
44 C3 H3A C H sing 1.09 N N
45 C3 H3B C H sing 1.09 N N
46 N6 HN6 N H sing 0.97 N N
47 N6 HN6A N H sing 0.97 N N
48 C8 H8 C H sing 1.08 N N
49 CA HA C H sing 1.09 N N
50 CB HB C H sing 1.09 N N
51 CB HBA C H sing 1.09 N N
52 C1' H1' C H sing 1.09 N N
53 C2' H2' C H sing 1.09 N N
54 O2' HO2' O H sing 0.97 N N
55 C3' H3' C H sing 1.09 N N
56 O3' HO3' O H sing 0.97 N N
57 C4' H4' C H sing 1.09 N N
58 C5' H5' C H sing 1.09 N N
59 C5' H5'A C H sing 1.09 N N
60 CAM HAM C H sing 1.09 N N
61 CAM HAMA C H sing 1.09 N N
62 CAN HAN C H sing 1.09 N N
63 CAN HANA C H sing 1.09 N N
64 CAO HAO C H sing 1.09 N N
65 CAO HAOA C H sing 1.09 N N
66 NAW HNAW N H sing 0.97 N N
67 CBF HBF C H sing 1.09 N N
68 CBF HBFA C H sing 1.09 N N
69 CBK HBK C H sing 1.09 N N
70 CBK HBKA C H sing 1.09 N N
71 OAI HAI O H sing 0.97 N N



YLB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YLB 4ch3 Open in New Window Bound ligand 1 1