Chemical Components in the PDB

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GKH : Summary

Code

GKH

One-letter code

X

Molecule name

[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate

Formula

C23 H20 N8 O8 S3

Formal charge

0

Molecular weight

632.649 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[S](=O)(=O)NC(=O)c4csc(C=Cc5sc6cc(O)ccc6n5)n4)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.6 c1cc2c(cc1O)sc(n2)C=Cc3nc(cs3)C(=O)NS(=O)(=O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)c4csc(/C=C/c5sc6cc(O)ccc6n5)n4)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc2c(cc1O)sc(n2)/C=C/c3nc(cs3)C(=O)NS(=O)(=O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O

IUPAC InChI

InChI=1S/C23H20N8O8S3/c24-20-17-21(26-8-25-20)31(9-27-17)23-19(34)18(33)13(39-23)6-38-42(36,37)30-22(35)12-7-40-15(29-12)3-4-16-28-11-2-1-10(32)5-14(11)41-16/h1-5,7-9,13,18-19,23,32-34H,6H2,(H,30,35)(H2,24,25,26)/b4-3+/t13-,18-,19-,23-/m1/s1

IUPAC InChI key

JXXQGJFRVFVJAK-AWGXURSZSA-N
GKH

wwPDB Information

Atom count

62 (42 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-09-21

Last modified at

2019-10-18

Status

Released

Obsoleted

Not Assigned



GKH : Atoms of Molecule

Total Number of Atoms: 62
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 -7.602 3.921 0.021
2 C4 C C2 N Y N 0 -5.736 2.58 -0.028
3 C5 C C3 N Y N 0 -4.986 3.621 0.545
4 C6 C C4 N Y N 0 -5.644 4.828 0.839
5 N9 N N1 N Y N 0 -4.862 1.538 -0.206
6 NBO N N2 N Y N 0 6.293 0.177 -0.578
7 CAE C C5 N Y N 0 7.45 0.554 -1.132
8 CAD C C6 N Y N 0 8.003 0.165 -2.373
9 CAC C C7 N Y N 0 9.206 0.655 -2.78
10 CAB C C8 N Y N 0 9.916 1.549 -1.983
11 OAA O O1 N N N 0 11.116 2.03 -2.404
12 CBP C C9 N Y N 0 9.4 1.947 -0.765
13 CAF C C10 N Y N 0 8.17 1.454 -0.335
14 SAG S S1 N Y N 0 7.249 1.754 1.137
15 CAH C C11 N Y N 0 5.985 0.665 0.58
16 CAI C C12 N N N 0 4.759 0.357 1.321
17 CAJ C C13 N N N 0 3.852 -0.496 0.8
18 CAK C C14 N Y N 0 2.626 -0.805 1.541
19 NAL N N3 N Y N 0 1.689 -1.614 1.138
20 SBN S S2 N Y N 0 2.198 -0.146 3.115
21 CBM C C15 N Y N 0 0.736 -1.033 3.11
22 CAM C C16 N Y N 0 0.659 -1.757 1.957
23 CAN C C17 N N N 0 -0.484 -2.635 1.647
24 OBL O O2 N N N 0 -1.406 -2.733 2.433
25 NAO N N4 N N N 0 -0.506 -3.331 0.493
26 SAP S S3 N N N 0 -1.789 -4.317 0.145
27 OBJ O O3 N N N 0 -1.532 -4.873 -1.138
28 OBK O O4 N N N 0 -2.013 -5.108 1.304
29 O5' O O5 N N N 0 -3.013 -3.426 -0.011
30 C5' C C18 N N N 0 -3.048 -2.695 -1.238
31 C4' C C19 R N N 0 -4.315 -1.838 -1.285
32 O4' O O6 N N N 0 -4.231 -0.763 -0.325
33 C3' C C20 S N N 0 -4.437 -1.135 -2.655
34 O3' O O7 N N N 0 -5.328 -1.854 -3.51
35 C2' C C21 R N N 0 -5.02 0.255 -2.313
36 O2' O O8 N N N 0 -6.287 0.437 -2.948
37 C1' C C22 R N N 0 -5.181 0.227 -0.777
38 C8 C C23 N Y N 0 -3.642 1.946 0.244
39 N7 N N5 N Y N 0 -3.717 3.169 0.684
40 N3 N N6 N Y N 0 -7.029 2.772 -0.27
41 N1 N N7 N Y N 0 -6.939 4.927 0.561
42 N6 N N8 N N N 0 -4.957 5.888 1.404
43 H1 H H1 N N N 0 -8.653 4.045 -0.192
44 H2 H H2 N N N 0 7.467 -0.527 -3.004
45 H3 H H3 N N N 0 9.614 0.347 -3.731
46 H4 H H4 N N N 0 11.054 2.846 -2.92
47 H5 H H5 N N N 0 9.95 2.641 -0.146
48 H6 H H6 N N N 0 4.582 0.811 2.285
49 H7 H H7 N N N 0 4.03 -0.951 -0.163
50 H8 H H8 N N N 0 -0.006 -1.024 3.895
51 H9 H H9 N N N 0 0.231 -3.253 -0.134
52 H10 H H10 N N N 0 -2.171 -2.051 -1.302
53 H11 H H11 N N N 0 -3.049 -3.392 -2.076
54 H12 H H12 N N N 0 -5.195 -2.452 -1.094
55 H13 H H13 N N N 0 -3.457 -1.036 -3.123
56 H14 H H14 N N N 0 -5.442 -1.457 -4.384
57 H15 H H15 N N N 0 -4.328 1.043 -2.61
58 H16 H H16 N N N 0 -6.251 0.403 -3.914
59 H17 H H17 N N N 0 -6.194 -0.068 -0.505
60 H18 H H18 N N N 0 -2.745 1.345 0.236
61 H19 H H19 N N N 0 -4.012 5.803 1.603
62 H20 H H20 N N N 0 -5.422 6.716 1.602



GKH : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N3 C N doub 1.32 N Y
2 C2 N1 C N sing 1.32 N Y
3 N3 C4 N C sing 1.33 N Y
4 N1 C6 N C doub 1.33 N Y
5 C1' N9 C N sing 1.47 N N
6 C1' O4' C O sing 1.44 N N
7 C1' C2' C C sing 1.54 N N
8 C4 N9 C N sing 1.37 N Y
9 C4 C5 C C doub 1.41 N Y
10 O2' C2' O C sing 1.43 N N
11 N9 C8 N C sing 1.36 N Y
12 O4' C4' O C sing 1.44 N N
13 C6 C5 C C sing 1.41 N Y
14 C6 N6 C N sing 1.38 N N
15 C5 N7 C N sing 1.35 N Y
16 OBK SAP O S doub 1.42 N N
17 OBL CAN O C doub 1.22 N N
18 C8 N7 C N doub 1.3 N Y
19 C2' C3' C C sing 1.55 N N
20 O5' SAP O S sing 1.52 N N
21 O5' C5' O C sing 1.43 N N
22 C4' C5' C C sing 1.53 N N
23 C4' C3' C C sing 1.54 N N
24 SAP NAO S N sing 1.66 N N
25 SAP OBJ S O doub 1.42 N N
26 CAN NAO C N sing 1.35 N N
27 CAN CAM C C sing 1.47 N N
28 C3' O3' C O sing 1.43 N N
29 SAG CAF S C sing 1.76 N Y
30 SAG CAH S C sing 1.76 N Y
31 CAM NAL C N sing 1.32 N Y
32 CAM CBM C C doub 1.36 N Y
33 CAI CAH C C sing 1.47 N N
34 CAI CAJ C C doub 1.35 E N
35 CBP CAF C C doub 1.39 N Y
36 CBP CAB C C sing 1.38 N Y
37 NAL CAK N C doub 1.3 N Y
38 CAF CAE C C sing 1.4 N Y
39 CAH NBO C N doub 1.29 N Y
40 OAA CAB O C sing 1.36 N N
41 CBM SBN C S sing 1.71 N Y
42 CAB CAC C C doub 1.39 N Y
43 CAK CAJ C C sing 1.47 N N
44 CAK SBN C S sing 1.76 N Y
45 CAE NBO C N sing 1.34 N Y
46 CAE CAD C C doub 1.41 N Y
47 CAC CAD C C sing 1.36 N Y
48 C2 H1 C H sing 1.08 N N
49 CAD H2 C H sing 1.08 N N
50 CAC H3 C H sing 1.08 N N
51 OAA H4 O H sing 0.97 N N
52 CBP H5 C H sing 1.08 N N
53 CAI H6 C H sing 1.08 N N
54 CAJ H7 C H sing 1.08 N N
55 CBM H8 C H sing 1.08 N N
56 NAO H9 N H sing 0.97 N N
57 C5' H10 C H sing 1.09 N N
58 C5' H11 C H sing 1.09 N N
59 C4' H12 C H sing 1.09 N N
60 C3' H13 C H sing 1.09 N N
61 O3' H14 O H sing 0.97 N N
62 C2' H15 C H sing 1.09 N N
63 O2' H16 O H sing 0.97 N N
64 C1' H17 C H sing 1.09 N N
65 C8 H18 C H sing 1.08 N N
66 N6 H19 N H sing 0.97 N N
67 N6 H20 N H sing 0.97 N N



GKH : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GKH 6hps Open in New Window Bound ligand 2 1