Chemical Components in the PDB

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YLA : Summary

Code

YLA

One-letter code

X

Molecule name

(S)-2-amino-6-(((prop-2-yn-1-yloxy)carbonyl)amino)hexanoic (((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric)anhydride

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-O-({[(2R)-2-amino-6-{[(prop-2-yn-1-yloxy)carbonyl]amino}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-(prop-2-ynoxycarbonylamino)hexanoate

Formula

C20 H28 N7 O10 P

Formal charge

0

Molecular weight

557.451 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCC#C)NCCCCC(N)C(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.385 N[CH](CCCCNC(=O)OCC#C)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.7.6 C#CCOC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
Canonical SMILES CACTVS 3.385 N[C@H](CCCCNC(=O)OCC#C)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 C#CCOC(=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/C20H28N7O10P/c1-2-7-34-20(31)23-6-4-3-5-11(21)19(30)37-38(32,33)35-8-12-14(28)15(29)18(36-12)27-10-26-13-16(22)24-9-25-17(13)27/h1,9-12,14-15,18,28-29H,3-8,21H2,(H,23,31)(H,32,33)(H2,22,24,25)/p-1/t11-,12-,14-,15-,18-/m1/s1

IUPAC InChI key

BXXVGWFYYCXKTG-AJKMGBEJSA-M
YLA

wwPDB Information

Atom count

66 (38 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



YLA : Atoms of Molecule

Total Number of Atoms: 66
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 1.963 -2.323 -1.4
2 N N N N N N 0 3.724 -2.28 -3.074
3 O O O N N N 0 1.882 -3.51 -1.609
4 N1 N N1 N Y N 0 -8.806 3.522 -0.61
5 O1 O O1 N N N 0 10.448 1.868 0.933
6 C2 C C2 N Y N 0 -8.436 3.283 0.635
7 C3 C C3 N N N 0 11.586 2.706 0.601
8 N3 N N3 N Y N 0 -7.444 2.47 0.934
9 C4 C C4 N Y N 0 -6.767 1.847 -0.025
10 C5 C C5 N Y N 0 -7.122 2.068 -1.366
11 C6 C C6 N Y N 0 -8.187 2.945 -1.635
12 N6 N N6 N N N 0 -8.583 3.201 -2.936
13 C7 C C7 N N N 0 12.482 2.802 1.765
14 N7 N N7 N Y N 0 -6.285 1.324 -2.129
15 C8 C C8 N Y N 0 -5.459 0.677 -1.36
16 C9 C C9 N N N 0 13.196 2.878 2.693
17 N9 N N9 N Y N 0 -5.715 0.966 -0.052
18 CA C CA R N N 0 3.121 -1.537 -1.96
19 CB C CB N N N 0 4.167 -1.32 -0.865
20 C1' C C1' R N N 0 -5.0 0.434 1.11
21 C2' C C2' R N N 0 -5.734 -0.804 1.684
22 O2' O O2' N N N 0 -6.747 -0.411 2.612
23 C3' C C3' S N N 0 -4.588 -1.556 2.403
24 O3' O O3' N N N 0 -4.594 -1.259 3.8
25 C4' C C4' R N N 0 -3.306 -1.014 1.741
26 O4' O O4' N N N 0 -3.712 -0.089 0.718
27 C5' C C5' N N N 0 -2.516 -2.166 1.117
28 O5' O O5' N N N 0 -1.275 -1.671 0.609
29 OAD O OAD N N N 0 9.67 2.196 -1.119
30 OAF O OAF N N N 0 -0.828 -3.326 -1.244
31 OAI O OAI N N N 0 0.388 -3.68 0.939
32 CAM C CAM N N N 0 6.329 -0.201 -0.303
33 CAN C CAN N N N 0 5.282 -0.418 -1.398
34 CAO C CAO N N N 0 7.444 0.702 -0.835
35 NAW N NAW N N N 0 8.446 0.91 0.214
36 OAY O OAY N N N 0 1.019 -1.703 -0.675
37 CBA C CBA N N N 0 9.527 1.677 -0.03
38 PBN P PBN N N N 0 -0.188 -2.611 -0.117
39 HN H HN N N N 0 4.062 -3.18 -2.767
40 HNA H HNA N N N 0 3.072 -2.381 -3.838
41 H2 H H2 N N N 0 -8.965 3.774 1.438
42 H3 H H3 N N N 0 12.126 2.268 -0.239
43 H3A H H3A N N N 0 11.236 3.701 0.328
44 HN6 H HN6 N N N 0 -9.32 3.807 -3.108
45 HN6A H HN6A N N N 0 -8.123 2.773 -3.676
46 H8 H H8 N N N 0 -4.685 0.008 -1.706
47 H9 H H9 N N N 0 13.835 2.946 3.524
48 HA H HA N N N 0 2.764 -0.571 -2.319
49 HB H HB N N N 0 3.698 -0.848 -0.003
50 HBA H HBA N N N 0 4.588 -2.281 -0.569
51 H1' H H1' N N N 0 -4.887 1.203 1.875
52 H2' H H2' N N N 0 -6.157 -1.411 0.883
53 HO2' H HO2' N N N 0 -7.235 -1.151 2.998
54 H3' H H3' N N N 0 -4.677 -2.631 2.242
55 HO3' H HO3' N N N 0 -5.404 -1.526 4.256
56 H4' H H4' N N N 0 -2.695 -0.501 2.483
57 H5' H H5' N N N 0 -2.321 -2.925 1.874
58 H5'A H H5'A N N N 0 -3.093 -2.604 0.303
59 HAM H HAM N N N 0 5.859 0.272 0.56
60 HAMA H HAMA N N N 0 6.749 -1.162 -0.007
61 HAN H HAN N N N 0 5.752 -0.89 -2.26
62 HANA H HANA N N N 0 4.862 0.543 -1.694
63 HAO H HAO N N N 0 7.913 0.229 -1.697
64 HAOA H HAOA N N N 0 7.023 1.663 -1.131
65 HNAW H HNAW N N N 0 8.331 0.495 1.083
66 HAI H HAI N N N 0 0.822 -3.281 1.706



YLA : Chemical Bonds

Total Number of Bonds: 68
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 O1 C3 O C sing 1.45 N N
8 O1 CBA O C sing 1.35 N N
9 C2 N3 C N sing 1.32 N Y
10 C3 C7 C C sing 1.47 N N
11 N3 C4 N C doub 1.33 N Y
12 C4 C5 C C sing 1.4 N Y
13 C4 N9 C N sing 1.37 N Y
14 C5 C6 C C doub 1.41 N Y
15 C5 N7 C N sing 1.36 N Y
16 C6 N6 C N sing 1.38 N N
17 C7 C9 C C trip 1.17 N N
18 N7 C8 N C doub 1.3 N Y
19 C8 N9 C N sing 1.36 N Y
20 N9 C1' N C sing 1.46 N N
21 CA CB C C sing 1.53 N N
22 CB CAN C C sing 1.53 N N
23 C1' C2' C C sing 1.55 N N
24 C1' O4' C O sing 1.44 N N
25 C2' O2' C O sing 1.43 N N
26 C2' C3' C C sing 1.55 N N
27 C3' O3' C O sing 1.43 N N
28 C3' C4' C C sing 1.54 N N
29 C4' O4' C O sing 1.44 N N
30 C4' C5' C C sing 1.53 N N
31 C5' O5' C O sing 1.43 N N
32 O5' PBN O P sing 1.61 N N
33 OAD CBA O C doub 1.21 N N
34 OAF PBN O P doub 1.48 N N
35 OAI PBN O P sing 1.61 N N
36 CAM CAN C C sing 1.53 N N
37 CAM CAO C C sing 1.53 N N
38 CAO NAW C N sing 1.47 N N
39 NAW CBA N C sing 1.35 N N
40 OAY PBN O P sing 1.61 N N
41 N HN N H sing 1.01 N N
42 N HNA N H sing 1.01 N N
43 C2 H2 C H sing 1.08 N N
44 C3 H3 C H sing 1.09 N N
45 C3 H3A 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 C9 H9 C H sing 1.05 N N
50 CA HA C H sing 1.09 N N
51 CB HB C H sing 1.09 N N
52 CB HBA C H sing 1.09 N N
53 C1' H1' C H sing 1.09 N N
54 C2' H2' C H sing 1.09 N N
55 O2' HO2' O H sing 0.97 N N
56 C3' H3' C H sing 1.09 N N
57 O3' HO3' O H sing 0.97 N N
58 C4' H4' C H sing 1.09 N N
59 C5' H5' C H sing 1.09 N N
60 C5' H5'A C H sing 1.09 N N
61 CAM HAM C H sing 1.09 N N
62 CAM HAMA C H sing 1.09 N N
63 CAN HAN C H sing 1.09 N N
64 CAN HANA C H sing 1.09 N N
65 CAO HAO C H sing 1.09 N N
66 CAO HAOA C H sing 1.09 N N
67 NAW HNAW N H sing 0.97 N N
68 OAI HAI O H sing 0.97 N N



YLA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YLA 4ch6 Open in New Window Bound ligand 1 1