Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

590 : Summary

Code

590

One-letter code

X

Molecule name

9-[2-azido-2-deoxy-5-O-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamoyl)-beta-D-arabinofuranosyl]-9H-purin-6-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 9-[2-azido-2-deoxy-5-O-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamoyl)-beta-D-arabinofuranosyl]-9H-purin-6-amine
OpenEye OEToolkits 1.9.2 [(2R,3S,5R)-5-(6-aminopurin-9-yl)-4-azido-3-oxidanyl-oxolan-2-yl]methyl N-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoyl]sulfamate

Formula

C20 H27 N11 O7 S2

Formal charge

0

Molecular weight

597.628 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NC2C(SCC2N1)CCCCC(=O)NS(=O)(=O)OCC5OC(n3c4ncnc(N)c4nc3)C(\N=[N+]=[N-])C5O
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[S](=O)(=O)NC(=O)CCCC[CH]4SC[CH]5NC(=O)N[CH]45)[CH](O)[CH]3N=[N+]=[N-]
SMILES OpenEye OEToolkits 1.9.2 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)CCCCC4C5C(CS4)NC(=O)N5)O)N=[N+]=[N-])N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)CCCC[C@@H]4SC[C@@H]5NC(=O)N[C@H]45)[C@@H](O)[C@@H]3N=[N+]=[N-]
Canonical SMILES OpenEye OEToolkits 1.9.2 c1nc(c2c(n1)n(cn2)[C@H]3C([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)CCCC[C@H]4[C@@H]5[C@H](CS4)NC(=O)N5)O)N=[N+]=[N-])N

IUPAC InChI

InChI=1S/C20H27N11O7S2/c21-17-15-18(24-7-23-17)31(8-25-15)19-14(28-30-22)16(33)10(38-19)5-37-40(35,36)29-12(32)4-2-1-3-11-13-9(6-39-11)26-20(34)27-13/h7-11,13-14,16,19,33H,1-6H2,(H,29,32)(H2,21,23,24)(H2,26,27,34)/t9-,10+,11-,13-,14-,16+,19+/m0/s1

IUPAC InChI key

UYTYJXXHSCNPCG-ROPJLRCXSA-N
590

wwPDB Information

Atom count

67 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-02-04

Last modified at

2015-08-28

Status

Released

Obsoleted

Not Assigned



590 : Atoms of Molecule

Total Number of Atoms: 67
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CBI C C1 S N N 0 6.458 1.875 -0.401
2 NAU N N1 N N N 0 6.474 1.606 1.045
3 CBA C C2 N N N 0 7.743 1.461 1.449
4 OAC O O1 N N N 0 8.05 1.23 2.603
5 NAT N N2 N N N 0 8.644 1.592 0.466
6 CBF C C3 R N N 0 7.94 1.865 -0.797
7 CAO C C4 N N N 0 8.269 0.753 -1.812
8 SAY S S1 N N N 0 6.942 -0.482 -1.504
9 CBH C C5 S N N 0 5.653 0.771 -1.114
10 CAK C C6 N N N 0 4.592 0.185 -0.181
11 CAI C C7 N N N 0 3.731 -0.817 -0.952
12 CAH C C8 N N N 0 2.67 -1.403 -0.019
13 CAJ C C9 N N N 0 1.809 -2.405 -0.79
14 CAZ C C10 N N N 0 0.763 -2.982 0.13
15 OAB O O2 N N N 0 0.713 -2.627 1.288
16 NAV N N3 N N N 0 -0.115 -3.892 -0.336
17 SBK S S2 N N N 0 -1.263 -4.527 0.675
18 OAD O O3 N N N 0 -2.043 -5.417 -0.112
19 OAE O O4 N N N 0 -0.581 -4.927 1.856
20 OAW O O5 N N N 0 -2.188 -3.387 1.078
21 CAN C C11 N N N 0 -3.096 -2.984 0.051
22 CBE C C12 R N N 0 -3.971 -1.839 0.564
23 OAX O O6 N N N 0 -3.185 -0.638 0.724
24 CAL C C13 S N N 0 -5.045 -1.471 -0.484
25 OAL O O7 N N N 0 -6.293 -2.088 -0.161
26 CAM C C14 S N N 0 -5.158 0.066 -0.382
27 CBG C C15 R N N 0 -4.139 0.445 0.716
28 N9 N N4 N Y N 0 -3.475 1.708 0.381
29 C8 C C16 N Y N 0 -2.311 1.847 -0.314
30 N7 N N5 N Y N 0 -2.01 3.108 -0.43
31 C5 C C17 N Y N 0 -2.96 3.856 0.181
32 C4 C C18 N Y N 0 -3.914 2.967 0.704
33 N3 N N6 N Y N 0 -4.964 3.456 1.355
34 C2 C C19 N Y N 0 -5.114 4.755 1.507
35 N1 N N7 N Y N 0 -4.246 5.629 1.031
36 C6 C C20 N Y N 0 -3.16 5.233 0.374
37 N6 N N8 N N N 0 -2.257 6.156 -0.122
38 N5 N N9 N N N -1 -6.09 0.382 -3.468
39 N2 N N10 N N N 1 -5.443 0.538 -2.562
40 H1 H H1 N N N 0 6.02 2.852 -0.604
41 H2 H H2 N N N 0 5.691 1.545 1.615
42 H3 H H3 N N N 0 9.606 1.52 0.57
43 H4 H H4 N N N 0 8.233 2.839 -1.189
44 H5 H H5 N N N 0 8.215 1.133 -2.832
45 H6 H H6 N N N 0 9.252 0.326 -1.612
46 H7 H H7 N N N 0 5.197 1.153 -2.027
47 H8 H H8 N N N 0 5.081 -0.321 0.652
48 H9 H H9 N N N 0 3.961 0.988 0.202
49 H10 H H10 N N N 0 3.243 -0.311 -1.785
50 H11 H H11 N N N 0 4.362 -1.62 -1.334
51 H12 H H12 N N N 0 3.158 -1.909 0.814
52 H16 H H16 N N N 0 -0.074 -4.176 -1.262
53 H13 H H13 N N N 0 2.039 -0.6 0.364
54 H14 H H14 N N N 0 1.32 -1.898 -1.623
55 H15 H H15 N N N 0 2.439 -3.207 -1.173
56 H17 H H17 N N N 0 -2.534 -2.65 -0.821
57 H18 H H18 N N N 0 -3.728 -3.828 -0.226
58 H19 H H19 N N N 0 -4.442 -2.115 1.508
59 H20 H H20 N N N 0 -4.72 -1.765 -1.483
60 H21 H H21 N N N 0 -7.003 -1.89 -0.787
61 H22 H H22 N N N 0 -6.166 0.356 -0.085
62 N8Q N N8Q N N N 0 -4.797 0.693 -1.656
63 H24 H H24 N N N 0 -4.635 0.522 1.683
64 H25 H H25 N N N 0 -1.724 1.031 -0.709
65 H26 H H26 N N N 0 -5.979 5.12 2.041
66 H27 H H27 N N N 0 -1.474 5.856 -0.609
67 H28 H H28 N N N 0 -2.406 7.105 0.018



590 : 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 OAD SBK O S doub 1.42 N N
2 OAE SBK O S doub 1.42 N N
3 SBK OAW S O sing 1.52 N N
4 SBK NAV S N sing 1.66 N N
5 OAW CAN O C sing 1.43 N N
6 OAL CAL O C sing 1.43 N N
7 NAV CAZ N C sing 1.35 N N
8 CBE CAN C C sing 1.53 N N
9 CBE CAL C C sing 1.55 N N
10 CBE OAX C O sing 1.44 N N
11 CAZ OAB C O doub 1.21 N N
12 CAZ CAJ C C sing 1.51 N N
13 CAL CAM C C sing 1.54 N N
14 OAX CBG O C sing 1.44 N N
15 CAM CBG C C sing 1.55 N N
16 CAJ CAH C C sing 1.53 N N
17 CBG N9 C N sing 1.47 N N
18 N5 N2 N N doub 1.12 N N
19 CAH CAI C C sing 1.53 N N
20 N9 C4 N C sing 1.37 N Y
21 N9 C8 N C sing 1.36 N Y
22 N3 C4 N C doub 1.33 N Y
23 N3 C2 N C sing 1.32 N Y
24 C4 C5 C C sing 1.4 N Y
25 CAI CAK C C sing 1.53 N N
26 C8 N7 C N doub 1.3 N Y
27 C2 N1 C N doub 1.32 N Y
28 C5 N7 C N sing 1.35 N Y
29 C5 C6 C C doub 1.4 N Y
30 CAK CBH C C sing 1.53 N N
31 N1 C6 N C sing 1.33 N Y
32 NAU CBI N C sing 1.47 N N
33 NAU CBA N C sing 1.34 N N
34 C6 N6 C N sing 1.38 N N
35 CBI CBH C C sing 1.54 N N
36 CBI CBF C C sing 1.53 N N
37 CBH SAY C S sing 1.84 N N
38 OAC CBA O C doub 1.22 N N
39 CBA NAT C N sing 1.34 N N
40 CBF NAT C N sing 1.47 N N
41 CBF CAO C C sing 1.54 N N
42 SAY CAO S C sing 1.84 N N
43 CBI H1 C H sing 1.09 N N
44 NAU H2 N H sing 0.97 N N
45 NAT H3 N H sing 0.97 N N
46 CBF H4 C H sing 1.09 N N
47 CAO H5 C H sing 1.09 N N
48 CAO H6 C H sing 1.09 N N
49 CBH H7 C H sing 1.09 N N
50 CAK H8 C H sing 1.09 N N
51 CAK H9 C H sing 1.09 N N
52 CAI H10 C H sing 1.09 N N
53 CAI H11 C H sing 1.09 N N
54 CAH H12 C H sing 1.09 N N
55 CAH H13 C H sing 1.09 N N
56 CAJ H14 C H sing 1.09 N N
57 CAJ H15 C H sing 1.09 N N
58 NAV H16 N H sing 0.97 N N
59 CAN H17 C H sing 1.09 N N
60 CAN H18 C H sing 1.09 N N
61 CBE H19 C H sing 1.09 N N
62 CAL H20 C H sing 1.09 N N
63 OAL H21 O H sing 0.97 N N
64 CAM H22 C H sing 1.09 N N
65 CAM N8Q C N sing 1.47 N N
66 CBG H24 C H sing 1.09 N N
67 C8 H25 C H sing 1.08 N N
68 C2 H26 C H sing 1.08 N N
69 N6 H27 N H sing 0.97 N N
70 N6 H28 N H sing 0.97 N N
71 N2 N8Q N N doub 1.12 N N



590 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
590 4xtx Open in New Window Bound ligand 2 1