Chemical Components in the PDB

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ZIT : Summary

Code

ZIT

One-letter code

X

Molecule name

AZITHROMYCIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside
OpenEye OEToolkits 1.5.0 (2R,3S,4R,5R,6R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-dimethylamino-3-hydroxy-6-methyl-oxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyl-oxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one

Formula

C38 H72 N2 O12

Formal charge

0

Molecular weight

748.984 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C3OC(CC)C(O)(C)C(O)C(N(C)CC(C)CC(O)(C)C(OC1OC(C)CC(N(C)C)C1O)C(C(OC2OC(C(O)C(OC)(C2)C)C)C3C)C)C
SMILES CACTVS 3.341 CC[CH]1OC(=O)[CH](C)[CH](O[CH]2C[C](C)(OC)[CH](O)[CH](C)O2)[CH](C)[CH](O[CH]3O[CH](C)C[CH]([CH]3O)N(C)C)[C](C)(O)C[CH](C)CN(C)[CH](C)[CH](O)[C]1(C)O
SMILES OpenEye OEToolkits 1.5.0 CCC1C(C(C(N(CC(CC(C(C(C(C(C(=O)O1)C)OC2CC(C(C(O2)C)O)(C)OC)C)OC3C(C(CC(O3)C)N(C)C)O)(C)O)C)C)C)O)(C)O
Canonical SMILES CACTVS 3.341 CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@H]2C[C@@](C)(OC)[C@@H](O)[C@H](C)O2)[C@H](C)[C@@H](O[C@@H]3O[C@H](C)C[C@@H]([C@H]3O)N(C)C)[C@](C)(O)C[C@@H](C)CN(C)[C@H](C)[C@@H](O)[C@]1(C)O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC[C@@H]1[C@@]([C@@H]([C@H]([N@@](C[C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)C)O)(C)O

IUPAC InChI

InChI=1S/C38H72N2O12/c1-15-27-38(10,46)31(42)24(6)40(13)19-20(2)17-36(8,45)33(52-35-29(41)26(39(11)12)16-21(3)48-35)22(4)30(23(5)34(44)50-27)51-28-18-37(9,47-14)32(43)25(7)49-28/h20-33,35,41-43,45-46H,15-19H2,1-14H3/t20-,21-,22+,23-,24-,25+,26+,27-,28+,29-,30+,31-,32+,33-,35+,36-,37-,38-/m1/s1

IUPAC InChI key

MQTOSJVFKKJCRP-BICOPXKESA-N
ZIT

wwPDB Information

Atom count

124 (52 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2002-06-20

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



ZIT : Atoms of Molecule

Total Number of Atoms: 124
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 1.922 -1.06 2.146
2 C2 C C2 R N N 0 1.29 -2.256 1.465
3 C3 C C3 S N N 0 0.72 -1.813 0.121
4 C4 C C4 S N N 0 -0.604 -2.501 -0.175
5 C5 C C5 R N N 0 -1.709 -1.445 -0.269
6 C6 C C6 R N N 0 -2.736 -1.601 0.859
7 C7 C C7 N N N 0 -3.664 -0.392 0.816
8 C8 C C8 R N N 0 -4.069 0.183 2.174
9 C9 C C9 N N N 0 -2.873 0.866 2.785
10 N10 N N10 N N N 0 -2.852 1.123 4.249
11 C11 C C11 R N N 0 -1.511 1.77 4.486
12 C12 C C12 R N N 0 -0.334 1.088 3.833
13 C13 C C13 S N N 0 0.947 1.288 4.655
14 C14 C C14 R N N 0 2.083 0.42 4.081
15 C15 C C15 N N N 0 2.953 -0.114 5.23
16 C16 C C16 N N N 0 4.099 -0.95 4.656
17 C17 C C17 N N N 0 2.342 -3.339 1.248
18 C18 C C18 N N N 0 -0.506 -3.206 -1.542
19 C19 C C19 N N N 0 -1.996 -1.807 2.174
20 C20 C C20 N N N 0 -4.842 -0.83 3.006
21 C21 C C21 N N N 0 -2.592 -0.208 4.893
22 C22 C C22 N N N 0 -1.597 3.232 4.01
23 C23 C C23 N N N 0 0.779 0.916 6.127
24 O1 O O1 N N N 0 2.826 -0.473 1.581
25 O6 O O6 N N N 0 -3.511 -2.803 0.625
26 O12 O O12 N N N 0 -0.117 1.732 2.554
27 O13 O O13 N N N 0 1.362 2.66 4.569
28 O14 O O14 N N N 0 1.502 -0.692 3.359
29 C1A C C1A S N N 0 -1.896 -0.456 -2.33
30 C2A C C2A R N N 0 -2.491 -0.561 -3.736
31 C3A C C3A S N N 0 -1.951 0.588 -4.593
32 C4A C C4A N N N 0 -2.225 1.91 -3.867
33 C5A C C5A R N N 0 -1.651 1.829 -2.45
34 C6A C C6A N N N 0 -1.891 3.157 -1.729
35 C7A C C7A N N N 0 -4.016 1.005 -5.652
36 C8A C C8A N N N 0 -2.005 1.662 -6.691
37 O1A O O1A N N N 0 -2.367 -1.544 -1.532
38 O2A O O2A N N N 0 -2.117 -1.81 -4.321
39 N3A N N3A N N N 0 -2.627 0.594 -5.898
40 O5A O O5A N N N 0 -2.289 0.776 -1.73
41 C1B C C1B R N N 0 2.29 -0.869 -1.276
42 C2B C C2B N N N 0 3.534 -1.177 -2.11
43 C3B C C3B R N N 0 4.236 0.121 -2.501
44 C4B C C4B S N N 0 3.25 1.134 -3.066
45 C5B C C5B S N N 0 1.912 1.173 -2.352
46 C6B C C6B N N N 0 1.963 2.075 -1.119
47 C7B C C7B N N N 0 4.988 0.699 -1.299
48 C8B C C8B N N N 0 5.931 1.021 -3.777
49 O1B O O1B N N N 0 1.66 -2.11 -0.921
50 O3B O O3B N N N 0 5.208 -0.184 -3.522
51 O4B O O4B N N N 0 3.033 0.85 -4.458
52 O5B O O5B N N N 0 1.381 -0.096 -2.041
53 H2 H H2 N N N 0 0.496 -2.638 2.108
54 H3 H H3 N N N 0 0.551 -0.72 0.136
55 H4 H H4 N N N 0 -0.82 -3.256 0.575
56 H5 H H5 N N N 0 -1.249 -0.455 -0.18
57 H71 H 1H7 N N N 0 -3.132 0.422 0.288
58 H72 H 2H7 N N N 0 -4.552 -0.627 0.209
59 H8 H H8 N N N 0 -4.834 0.98 1.934
60 H91 H 1H9 N N N 0 -1.954 0.45 2.473
61 H92 H 2H9 N N N 0 -2.888 1.886 2.31
62 H11 H H11 N N N 0 -1.419 1.789 5.58
63 H12 H H12 N N N 0 -0.478 0.031 3.622
64 H14 H H14 N N N 0 2.705 1.036 3.435
65 H151 H 1H15 N N N 0 2.345 -0.735 5.888
66 H152 H 2H15 N N N 0 3.362 0.722 5.796
67 H161 H 1H16 N N N 0 4.716 -1.329 5.471
68 H162 H 2H16 N N N 0 3.69 -1.787 4.09
69 H163 H 3H16 N N N 0 4.707 -0.329 3.998
70 H171 H 1H17 N N N 0 2.752 -3.646 2.21
71 H172 H 2H17 N N N 0 1.884 -4.198 0.757
72 H173 H 3H17 N N N 0 3.143 -2.947 0.621
73 H181 H 1H18 N N N 0 0.263 -3.976 -1.499
74 H182 H 2H18 N N N 0 -1.465 -3.663 -1.785
75 H183 H 3H18 N N N 0 -0.247 -2.476 -2.309
76 H191 H 1H19 N N N 0 -1.235 -1.035 2.289
77 H192 H 2H19 N N N 0 -2.702 -1.747 3.002
78 H193 H 3H19 N N N 0 -1.52 -2.788 2.173
79 H201 H 1H20 N N N 0 -5.063 -0.403 3.985
80 H202 H 2H20 N N N 0 -5.774 -1.08 2.5
81 H203 H 3H20 N N N 0 -4.242 -1.732 3.13
82 H211 H 1H21 N N N 0 -1.713 -0.665 4.439
83 H212 H 2H21 N N N 0 -2.419 -0.067 5.96
84 H213 H 3H21 N N N 0 -3.456 -0.856 4.747
85 H221 H 1H22 N N N 0 -2.371 3.752 4.574
86 H222 H 2H22 N N N 0 -0.638 3.724 4.171
87 H223 H 3H22 N N N 0 -1.844 3.254 2.948
88 H231 H 1H23 N N N 0 1.721 1.079 6.652
89 H232 H 2H23 N N N 0 0.0020 1.537 6.573
90 H233 H 3H23 N N N 0 0.496 -0.133 6.207
91 HO6 H HO6 N N N 0 -4.146 -2.872 1.35
92 HO12 H HO12 N N N 0 0.671 1.329 2.168
93 HO13 H HO13 N N N 0 2.168 2.742 5.097
94 H1A1 H 1H1A N N N 0 -0.808 -0.498 -2.392
95 H2A1 H 1H2A N N N 0 -3.577 -0.495 -3.679
96 H3A1 H 1H3A N N N 0 -0.878 0.466 -4.738
97 H4A1 H 1H4A N N N 0 -3.3 2.082 -3.815
98 H4A2 H 2H4A N N N 0 -1.749 2.729 -4.407
99 H5A1 H 1H5A N N N 0 -0.58 1.634 -2.504
100 H6A1 H 1C6A N N N 0 -1.478 3.102 -0.722
101 H6A2 H 2C6A N N N 0 -1.404 3.962 -2.279
102 H6A3 H 3C6A N N N 0 -2.962 3.351 -1.673
103 H7A1 H 1H7A N N N 0 -4.6 0.875 -6.563
104 H7A2 H 2H7A N N N 0 -4.441 0.391 -4.858
105 H7A3 H 3H7A N N N 0 -4.037 2.052 -5.353
106 H8A1 H 1H8A N N N 0 -2.466 1.697 -7.678
107 H8A2 H 2H8A N N N 0 -2.149 2.619 -6.188
108 H8A3 H 3H8A N N N 0 -0.938 1.464 -6.795
109 HO2A H HO2A N N N 0 -2.476 -2.504 -3.751
110 H1B1 H 1H1B N N N 0 2.572 -0.359 -0.359
111 H2B1 H 1H2B N N N 0 4.216 -1.8 -1.526
112 H2B2 H 2H2B N N N 0 3.242 -1.722 -3.01
113 H4B1 H 1H4B N N N 0 3.708 2.136 -3.008
114 H5B1 H 1H5B N N N 0 1.189 1.653 -3.054
115 H6B1 H 1C6B N N N 0 0.988 2.08 -0.631
116 H6B2 H 2C6B N N N 0 2.715 1.7 -0.425
117 H6B3 H 3C6B N N N 0 2.222 3.09 -1.422
118 H7B1 H 1H7B N N N 0 5.824 0.047 -1.046
119 H7B2 H 2H7B N N N 0 5.364 1.691 -1.549
120 H7B3 H 3H7B N N N 0 4.311 0.77 -0.448
121 H8B1 H 1H8B N N N 0 6.606 0.868 -4.619
122 H8B2 H 2H8B N N N 0 5.231 1.822 -4.014
123 H8B3 H 3H8B N N N 0 6.509 1.292 -2.893
124 HO4B H HO4B N N N 0 2.405 1.509 -4.783



ZIT : Chemical Bonds

Total Number of Bonds: 126
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C1 O1 C O doub 1.22 N N
3 C1 O14 C O sing 1.34 N N
4 C2 C3 C C sing 1.53 N N
5 C2 C17 C C sing 1.53 N N
6 C2 H2 C H sing 1.09 N N
7 C3 C4 C C sing 1.52 N N
8 C3 O1B C O sing 1.43 N N
9 C3 H3 C H sing 1.11 N N
10 C4 C5 C C sing 1.53 N N
11 C4 C18 C C sing 1.54 N N
12 C4 H4 C H sing 1.09 N N
13 C5 C6 C C sing 1.53 N N
14 C5 O1A C O sing 1.43 N N
15 C5 H5 C H sing 1.1 N N
16 C6 C7 C C sing 1.52 N N
17 C6 C19 C C sing 1.52 N N
18 C6 O6 C O sing 1.45 N N
19 C7 C8 C C sing 1.53 N N
20 C7 H71 C H sing 1.11 N N
21 C7 H72 C H sing 1.1 N N
22 C8 C9 C C sing 1.51 N N
23 C8 C20 C C sing 1.52 N N
24 C8 H8 C H sing 1.13 N N
25 C9 N10 C N sing 1.49 N N
26 C9 H91 C H sing 1.06 N N
27 C9 H92 C H sing 1.13 N N
28 N10 C11 N C sing 1.51 N N
29 N10 C21 N C sing 1.5 N N
30 C11 C12 C C sing 1.51 N N
31 C11 C22 C C sing 1.54 N N
32 C11 H11 C H sing 1.1 N N
33 C12 C13 C C sing 1.54 N N
34 C12 O12 C O sing 1.45 N N
35 C12 H12 C H sing 1.09 N N
36 C13 C14 C C sing 1.54 N N
37 C13 C23 C C sing 1.53 N N
38 C13 O13 C O sing 1.44 N N
39 C14 C15 C C sing 1.54 N N
40 C14 O14 C O sing 1.45 N N
41 C14 H14 C H sing 1.09 N N
42 C15 C16 C C sing 1.53 N N
43 C15 H151 C H sing 1.09 N N
44 C15 H152 C H sing 1.09 N N
45 C16 H161 C H sing 1.09 N N
46 C16 H162 C H sing 1.09 N N
47 C16 H163 C H sing 1.09 N N
48 C17 H171 C H sing 1.09 N N
49 C17 H172 C H sing 1.09 N N
50 C17 H173 C H sing 1.09 N N
51 C18 H181 C H sing 1.09 N N
52 C18 H182 C H sing 1.09 N N
53 C18 H183 C H sing 1.09 N N
54 C19 H191 C H sing 1.09 N N
55 C19 H192 C H sing 1.09 N N
56 C19 H193 C H sing 1.09 N N
57 C20 H201 C H sing 1.09 N N
58 C20 H202 C H sing 1.09 N N
59 C20 H203 C H sing 1.09 N N
60 C21 H211 C H sing 1.09 N N
61 C21 H212 C H sing 1.09 N N
62 C21 H213 C H sing 1.09 N N
63 C22 H221 C H sing 1.09 N N
64 C22 H222 C H sing 1.09 N N
65 C22 H223 C H sing 1.09 N N
66 C23 H231 C H sing 1.09 N N
67 C23 H232 C H sing 1.09 N N
68 C23 H233 C H sing 1.09 N N
69 O6 HO6 O H sing 0.97 N N
70 O12 HO12 O H sing 0.97 N N
71 O13 HO13 O H sing 0.97 N N
72 C1A C2A C C sing 1.53 N N
73 C1A O1A C O sing 1.43 N N
74 C1A O5A C O sing 1.43 N N
75 C1A H1A1 C H sing 1.09 N N
76 C2A C3A C C sing 1.53 N N
77 C2A O2A C O sing 1.43 N N
78 C2A H2A1 C H sing 1.09 N N
79 C3A C4A C C sing 1.53 N N
80 C3A N3A C N sing 1.47 N N
81 C3A H3A1 C H sing 1.09 N N
82 C4A C5A C C sing 1.53 N N
83 C4A H4A1 C H sing 1.09 N N
84 C4A H4A2 C H sing 1.09 N N
85 C5A C6A C C sing 1.53 N N
86 C5A O5A C O sing 1.43 N N
87 C5A H5A1 C H sing 1.09 N N
88 C6A H6A1 C H sing 1.09 N N
89 C6A H6A2 C H sing 1.09 N N
90 C6A H6A3 C H sing 1.09 N N
91 C7A N3A C N sing 1.47 N N
92 C7A H7A1 C H sing 1.09 N N
93 C7A H7A2 C H sing 1.09 N N
94 C7A H7A3 C H sing 1.09 N N
95 C8A N3A C N sing 1.47 N N
96 C8A H8A1 C H sing 1.09 N N
97 C8A H8A2 C H sing 1.09 N N
98 C8A H8A3 C H sing 1.09 N N
99 O2A HO2A O H sing 0.97 N N
100 C1B C2B C C sing 1.53 N N
101 C1B O1B C O sing 1.44 N N
102 C1B O5B C O sing 1.42 N N
103 C1B H1B1 C H sing 1.09 N N
104 C2B C3B C C sing 1.53 N N
105 C2B H2B1 C H sing 1.09 N N
106 C2B H2B2 C H sing 1.09 N N
107 C3B C4B C C sing 1.52 N N
108 C3B C7B C C sing 1.53 N N
109 C3B O3B C O sing 1.44 N N
110 C4B C5B C C sing 1.52 N N
111 C4B O4B C O sing 1.44 N N
112 C4B H4B1 C H sing 1.1 N N
113 C5B C6B C C sing 1.53 N N
114 C5B O5B C O sing 1.41 N N
115 C5B H5B1 C H sing 1.12 N N
116 C6B H6B1 C H sing 1.09 N N
117 C6B H6B2 C H sing 1.09 N N
118 C6B H6B3 C H sing 1.09 N N
119 C7B H7B1 C H sing 1.09 N N
120 C7B H7B2 C H sing 1.09 N N
121 C7B H7B3 C H sing 1.09 N N
122 C8B O3B C O sing 1.43 N N
123 C8B H8B1 C H sing 1.09 N N
124 C8B H8B2 C H sing 1.09 N N
125 C8B H8B3 C H sing 1.09 N N
126 O4B HO4B O H sing 0.97 N N



ZIT : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
ZIT 1m1k Open in New Window Bound ligand 1 1
ZIT 1nwy Open in New Window Bound ligand 2 1
ZIT 1yhq Open in New Window Bound ligand 1 1
ZIT 4v7y Open in New Window Bound ligand 2 1
ZIT 5igi Open in New Window Bound ligand 1 1
ZIT 5igv Open in New Window Bound ligand 1 1
ZIT 5uxc Open in New Window Bound ligand 2 1
ZIT 5uxd Open in New Window Bound ligand 3 1