Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

GMK : Summary

Code

GMK

One-letter code

X

Molecule name

(3-Deoxy-3-(3-methoxy-benzamido)-b-D-galactopyranosyl)-(3-deoxy-3-(3-methoxy-benzamido)-2-O-sulfo-b-D-galactopyranosyl)-sulfide

Systematic names

ProgramVersionName
ACDLabs 12.01 3-deoxy-3-[(3-methoxybenzoyl)amino]-beta-D-galactopyranosyl 3-deoxy-3-[(3-methoxybenzoyl)amino]-2-O-sulfo-1-thio-beta-D-galactopyranoside
OpenEye OEToolkits 1.9.2 [(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-2-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-4-[(3-methoxyphenyl)carbonylamino]-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-4-[(3-methoxyphenyl)carbonylamino]-5-oxidanyl-oxan-3-yl] hydrogen sulfate

Formula

C28 H36 N2 O15 S2

Formal charge

0

Molecular weight

704.72 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S(=O)(O)OC4C(NC(=O)c1cccc(OC)c1)C(O)C(OC4SC3OC(CO)C(O)C(NC(=O)c2cccc(OC)c2)C3O)CO
SMILES CACTVS 3.385 COc1cccc(c1)C(=O)N[CH]2[CH](O)[CH](CO)O[CH](S[CH]3O[CH](CO)[CH](O)[CH](NC(=O)c4cccc(OC)c4)[CH]3O[S](O)(=O)=O)[CH]2O
SMILES OpenEye OEToolkits 1.9.2 COc1cccc(c1)C(=O)NC2C(C(OC(C2O)SC3C(C(C(C(O3)CO)O)NC(=O)c4cccc(c4)OC)OS(=O)(=O)O)CO)O
Canonical SMILES CACTVS 3.385 COc1cccc(c1)C(=O)N[C@H]2[C@@H](O)[C@@H](CO)O[C@@H](S[C@@H]3O[C@H](CO)[C@H](O)[C@H](NC(=O)c4cccc(OC)c4)[C@H]3O[S](O)(=O)=O)[C@@H]2O
Canonical SMILES OpenEye OEToolkits 1.9.2 COc1cccc(c1)C(=O)N[C@H]2[C@H]([C@H](O[C@H]([C@@H]2O)S[C@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)NC(=O)c4cccc(c4)OC)OS(=O)(=O)O)CO)O

IUPAC InChI

InChI=1S/C28H36N2O15S2/c1-41-15-7-3-5-13(9-15)25(36)29-19-21(33)17(11-31)43-27(23(19)35)46-28-24(45-47(38,39)40)20(22(34)18(12-32)44-28)30-26(37)14-6-4-8-16(10-14)42-2/h3-10,17-24,27-28,31-35H,11-12H2,1-2H3,(H,29,36)(H,30,37)(H,38,39,40)/t17-,18-,19+,20+,21+,22+,23-,24-,27+,28+/m1/s1

IUPAC InChI key

CNUFQRWWCPUUQG-CWKIZLMASA-N
GMK

wwPDB Information

Atom count

83 (47 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-03

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



GMK : Atoms of Molecule

Total Number of Atoms: 83
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1G N N N 0 5.862 -0.21 -1.503
2 C1 C C1F N N N 0 6.287 -0.088 -0.371
3 C2 C C4F N Y N 0 7.572 0.605 -0.134
4 C3 C C5F N Y N 0 8.062 0.747 1.164
5 C4 C C6F N Y N 0 9.262 1.394 1.381
6 O2 O O1H N N N 0 10.21 2.269 -2.024
7 C5 C C1H N N N 0 11.442 2.925 -1.715
8 C6 C C1G N Y N 0 9.981 1.903 0.315
9 C7 C C2F N Y N 0 9.5 1.766 -0.98
10 C8 C C3F N Y N 0 8.301 1.114 -1.21
11 N1 N N1E N N N 0 5.585 -0.578 0.67
12 C9 C C4D S N N 0 4.309 -1.259 0.436
13 C10 C C5D R N N 0 4.021 -2.22 1.594
14 O3 O O2D N N N 0 4.021 -1.497 2.826
15 C11 C C1D R N N 0 2.651 -2.868 1.381
16 C12 C C1E N N N 0 2.33 -3.784 2.563
17 O4 O O1F N N N 0 1.106 -4.477 2.311
18 O5 O O1D N N N 0 1.654 -1.849 1.283
19 C13 C C3D R N N 0 3.183 -0.224 0.355
20 O6 O O1E N N N 0 3.403 0.634 -0.767
21 C14 C C2D S N N 0 1.844 -0.949 0.19
22 S1 S S1C N N N 0 0.498 0.266 0.164
23 C15 C C1C S N N 0 -0.963 -0.752 -0.186
24 C16 C C2C R N N 0 -2.22 0.119 -0.118
25 O7 O O4K N N N 0 -2.369 0.641 1.204
26 S2 S S2K N N N 0 -2.273 2.158 1.285
27 O8 O O2K N N N 0 -3.563 2.722 0.707
28 O9 O O1K N N N 0 -2.274 2.486 2.668
29 O10 O O3K N N N 0 -1.233 2.542 0.396
30 O11 O O5C N N N 0 -0.847 -1.318 -1.493
31 C17 C C5C R N N 0 -1.939 -2.163 -1.862
32 C18 C C6C N N N 0 -1.695 -2.732 -3.261
33 O12 O O6C N N N 0 -0.549 -3.586 -3.234
34 C19 C C4C R N N 0 -3.236 -1.349 -1.861
35 O13 O O4C N N N 0 -3.147 -0.308 -2.836
36 C20 C C3C S N N 0 -3.442 -0.734 -0.474
37 N2 N NA N N N 0 -4.641 0.109 -0.484
38 C21 C C1A N N N 0 -5.84 -0.422 -0.176
39 O14 O OA N N N 0 -5.928 -1.6 0.112
40 C22 C C2A N Y N 0 -7.05 0.428 -0.187
41 C23 C C3A N Y N 0 -6.953 1.779 -0.522
42 C24 C C4A N Y N 0 -8.084 2.57 -0.531
43 C25 C C5A N Y N 0 -9.315 2.027 -0.209
44 C26 C C6A N Y N 0 -9.421 0.684 0.126
45 C27 C C7A N Y N 0 -8.293 -0.119 0.132
46 O15 O O1A N N N 0 -10.633 0.157 0.443
47 C28 C C1B N N N 0 -11.754 1.042 0.41
48 H1 H H1 N N N 0 7.503 0.352 1.999
49 H2 H H2 N N N 0 9.64 1.503 2.387
50 H3 H H3 N N N 0 12.111 2.225 -1.216
51 H4 H H4 N N N 0 11.906 3.278 -2.636
52 H5 H H5 N N N 0 11.247 3.773 -1.058
53 H6 H H6 N N N 0 10.919 2.408 0.491
54 H7 H H7 N N N 0 7.928 1.003 -2.217
55 H8 H H8 N N N 0 5.924 -0.481 1.573
56 H9 H H9 N N N 0 4.359 -1.817 -0.499
57 H10 H H10 N N N 0 4.79 -2.993 1.625
58 H11 H H11 N N N 0 3.845 -2.045 3.603
59 H12 H H12 N N N 0 2.664 -3.453 0.461
60 H13 H H13 N N N 0 3.136 -4.507 2.692
61 H14 H H14 N N N 0 2.23 -3.187 3.469
62 H15 H H15 N N N 0 0.84 -5.077 3.021
63 H16 H H16 N N N 0 3.166 0.369 1.269
64 H17 H H17 N N N 0 2.726 1.315 -0.879
65 H18 H H18 N N N 0 1.847 -1.509 -0.746
66 H19 H H19 N N N 0 -1.034 -1.551 0.551
67 H20 H H20 N N N 0 -2.132 0.942 -0.827
68 H21 H H21 N N N 0 -2.023 -2.981 -1.146
69 H22 H H22 N N N 0 -2.567 -3.303 -3.578
70 H23 H H23 N N N 0 -1.522 -1.914 -3.96
71 H24 H H24 N N N 0 -0.335 -3.983 -4.09
72 H25 H H25 N N N 0 -4.076 -2.001 -2.1
73 H26 H H26 N N N 0 -3.01 -0.626 -3.739
74 H27 H H27 N N N 0 -3.561 -1.527 0.265
75 H28 H H28 N N N 0 -4.571 1.048 -0.714
76 H29 H H29 N N N 0 -5.994 2.206 -0.774
77 H30 H H30 N N N 0 -8.008 3.615 -0.791
78 H31 H H31 N N N 0 -10.197 2.651 -0.217
79 H32 H H32 N N N 0 -8.375 -1.166 0.389
80 H33 H H33 N N N 0 -11.595 1.856 1.118
81 H34 H H34 N N N 0 -11.866 1.45 -0.594
82 H35 H H35 N N N 0 -12.657 0.495 0.683
83 H36 H H36 N N N 0 -3.606 3.688 0.711



GMK : Chemical Bonds

Total Number of Bonds: 86
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O4 C12 O C sing 1.43 N N
2 C12 C11 C C sing 1.53 N N
3 O14 C21 O C doub 1.22 N N
4 O9 S2 O S doub 1.42 N N
5 C23 C24 C C doub 1.38 N Y
6 C23 C22 C C sing 1.4 N Y
7 C24 C25 C C sing 1.38 N Y
8 C21 C22 C C sing 1.48 N N
9 C21 N2 C N sing 1.35 N N
10 C22 C27 C C doub 1.39 N Y
11 O7 S2 O S sing 1.52 N N
12 O7 C16 O C sing 1.43 N N
13 C11 O5 C O sing 1.43 N N
14 C11 C10 C C sing 1.53 N N
15 C25 C26 C C doub 1.39 N Y
16 O5 C14 O C sing 1.43 N N
17 S2 O10 S O doub 1.42 N N
18 S2 O8 S O sing 1.52 N N
19 C27 C26 C C sing 1.38 N Y
20 C20 N2 C N sing 1.47 N N
21 C20 C16 C C sing 1.53 N N
22 C20 C19 C C sing 1.53 N N
23 C26 O15 C O sing 1.36 N N
24 C15 C16 C C sing 1.53 N N
25 C15 S1 C S sing 1.81 N N
26 C15 O11 C O sing 1.43 N N
27 C10 O3 C O sing 1.43 N N
28 C10 C9 C C sing 1.53 N N
29 C17 C19 C C sing 1.53 N N
30 C17 O11 C O sing 1.43 N N
31 C17 C18 C C sing 1.53 N N
32 C14 S1 C S sing 1.81 N N
33 C14 C13 C C sing 1.53 N N
34 O15 C28 O C sing 1.43 N N
35 C19 O13 C O sing 1.43 N N
36 O12 C18 O C sing 1.43 N N
37 C9 C13 C C sing 1.53 N N
38 C9 N1 C N sing 1.47 N N
39 C13 O6 C O sing 1.43 N N
40 O1 C1 O C doub 1.22 N N
41 N1 C1 N C sing 1.35 N N
42 C1 C2 C C sing 1.48 N N
43 C2 C3 C C doub 1.39 N Y
44 C2 C8 C C sing 1.4 N Y
45 C3 C4 C C sing 1.38 N Y
46 C8 C7 C C doub 1.38 N Y
47 C4 C6 C C doub 1.38 N Y
48 C7 C6 C C sing 1.39 N Y
49 C7 O2 C O sing 1.36 N N
50 C5 O2 C O sing 1.43 N N
51 C3 H1 C H sing 1.08 N N
52 C4 H2 C H sing 1.08 N N
53 C5 H3 C H sing 1.09 N N
54 C5 H4 C H sing 1.09 N N
55 C5 H5 C H sing 1.09 N N
56 C6 H6 C H sing 1.08 N N
57 C8 H7 C H sing 1.08 N N
58 N1 H8 N H sing 0.97 N N
59 C9 H9 C H sing 1.09 N N
60 C10 H10 C H sing 1.09 N N
61 O3 H11 O H sing 0.97 N N
62 C11 H12 C H sing 1.09 N N
63 C12 H13 C H sing 1.09 N N
64 C12 H14 C H sing 1.09 N N
65 O4 H15 O H sing 0.97 N N
66 C13 H16 C H sing 1.09 N N
67 O6 H17 O H sing 0.97 N N
68 C14 H18 C H sing 1.09 N N
69 C15 H19 C H sing 1.09 N N
70 C16 H20 C H sing 1.09 N N
71 C17 H21 C H sing 1.09 N N
72 C18 H22 C H sing 1.09 N N
73 C18 H23 C H sing 1.09 N N
74 O12 H24 O H sing 0.97 N N
75 C19 H25 C H sing 1.09 N N
76 O13 H26 O H sing 0.97 N N
77 C20 H27 C H sing 1.09 N N
78 N2 H28 N H sing 0.97 N N
79 C23 H29 C H sing 1.08 N N
80 C24 H30 C H sing 1.08 N N
81 C25 H31 C H sing 1.08 N N
82 C27 H32 C H sing 1.08 N N
83 C28 H33 C H sing 1.09 N N
84 C28 H34 C H sing 1.09 N N
85 C28 H35 C H sing 1.09 N N
86 O8 H36 O H sing 0.97 N N



GMK : Used in PDB Entries

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