Chemical Components in the PDB

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CTY : Summary

Code

CTY

One-letter code

X

Molecule name

CLARITHROMYCIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,4S,5S,6R,7R,9R,11R,12R,13S,14R)-6-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-14-ethyl-12,13-dihydroxy-4-{[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyltetrahydro-2H-pyran-2-yl]oxy}-7-methoxy-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione (non-preferred name)
OpenEye OEToolkits 1.5.0 (3R,4S,5S,6R,7R,9R,11R,12R,13S,14R)-6-[(2S,3R,4S,6R)-4-dimethylamino-3-hydroxy-6-methyl-oxan-2-yl]oxy-14-ethyl-12,13-dihydroxy-4-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyl-oxan-2-yl]oxy-7-methoxy-3,5,7,9,11,13-hexamethyl-1-oxacyclotetradecane-2,10-dione

Formula

C38 H69 N O13

Formal charge

0

Molecular weight

747.953 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C3OC(CC)C(O)(C)C(O)C(C(=O)C(C)CC(OC)(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)(C[CH](C)C(=O)[CH](C)[CH](O)[C]1(C)O)OC
SMILES OpenEye OEToolkits 1.5.0 CCC1C(C(C(C(=O)C(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)OC)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)(C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O)OC
Canonical SMILES OpenEye OEToolkits 1.5.0 CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[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)OC)C)C)O)(C)O

IUPAC InChI

InChI=1S/C38H69NO13/c1-15-26-38(10,45)31(42)21(4)28(40)19(2)17-37(9,47-14)33(52-35-29(41)25(39(11)12)16-20(3)48-35)22(5)30(23(6)34(44)50-26)51-27-18-36(8,46-13)32(43)24(7)49-27/h19-27,29-33,35,41-43,45H,15-18H2,1-14H3/t19-,20-,21+,22+,23-,24+,25+,26-,27+,29-,30+,31-,32+,33-,35+,36-,37-,38-/m1/s1

IUPAC InChI key

AGOYDEPGAOXOCK-KCBOHYOISA-N
CTY

wwPDB Information

Atom count

121 (52 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2001-09-18

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CTY : Atoms of Molecule

Total Number of Atoms: 121
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C10 R N N 0 1.652 4.666 5.666
2 C11 C C11 R N N 0 2.897 4.775 4.746
3 C12 C C12 S N N 0 4.302 4.553 5.391
4 C13 C C13 R N N 0 4.661 3.08 5.755
5 O2 O O2 N N N 0 4.251 2.233 4.651
6 C2 C C2 R N N 0 4.392 0.365 3.196
7 C3 C C3 S N N 0 2.871 0.113 3.321
8 C4 C C4 S N N 0 2.417 -0.568 4.642
9 C5 C C5 R N N 0 0.869 -0.752 4.763
10 C6 C C6 R N N 0 -0.034 0.513 4.587
11 C7 C C7 N N N 0 0.459 1.705 5.447
12 C8 C C8 R N N 0 -0.376 2.998 5.323
13 C9 C C9 N N N 0 0.463 4.177 4.824
14 O11 O O11 N N N 0 0.166 4.735 3.764
15 C1 C C1 N N N 0 4.967 1.103 4.393
16 O1 O O1 N N N 0 5.954 0.718 5.008
17 O3 O O3 N N N 0 2.427 -0.662 2.206
18 O7 O O7 N N N 0 0.59 -1.297 6.061
19 C34 C C34 N N N 0 1.229 5.979 6.334
20 C33 C C33 N N N 0 -1.077 3.35 6.632
21 C35 C C35 N N N 0 4.602 5.508 6.551
22 O12 O O12 N N N 0 2.869 6.075 4.133
23 O13 O O13 N N N 0 5.261 4.875 4.35
24 C36 C C36 N N N 0 4.076 2.512 7.044
25 C30 C C30 N N N 0 4.735 1.144 1.923
26 C32 C C32 N N N 0 -1.494 0.155 4.928
27 O10 O O10 N N N 0 -0.02 0.918 3.216
28 C22 C C22 S N N 0 0.016 -2.599 5.958
29 C23 C C23 R N N 0 0.423 -3.395 7.203
30 C24 C C24 S N N 0 -0.281 -4.758 7.237
31 C25 C C25 N N N 0 -1.786 -4.589 7.012
32 C26 C C26 R N N 0 -2.043 -3.766 5.749
33 O9 O O9 N N N 0 -1.403 -2.493 5.866
34 N1 N N1 N N N 0 -0.05 -5.431 8.516
35 C27 C C27 N N N 0 -3.532 -3.521 5.549
36 O8 O O8 N N N 0 1.837 -3.578 7.164
37 C28 C C28 N N N 0 -0.609 -4.644 9.614
38 C14 C C14 R N N 0 2.136 0.167 1.085
39 C15 C C15 N N N 0 3.054 -0.191 -0.089
40 C16 C C16 R N N 0 2.685 -1.539 -0.733
41 C17 C C17 S N N 0 1.17 -1.573 -1.018
42 C18 C C18 S N N 0 0.353 -1.178 0.22
43 O4 O O4 N N N 0 0.763 0.105 0.701
44 O5 O O5 N N N 0 3.039 -2.602 0.157
45 O6 O O6 N N N 0 0.764 -2.868 -1.451
46 C20 C C20 N N N 0 4.429 -2.596 0.434
47 C29 C C29 N N N 0 1.38 -5.655 8.722
48 C21 C C21 N N N 0 -1.138 -1.085 -0.097
49 C37 C C37 N N N 0 4.543 1.095 7.269
50 C31 C C31 N N N 0 3.114 -1.93 4.845
51 C19 C C19 N N N 0 3.509 -1.759 -2.004
52 C38 C C38 N N N 0 -0.462 -0.129 2.368
53 H10 H H10 N N N 0 1.835 3.919 6.442
54 H11 H H11 N N N 0 2.798 4.076 3.907
55 H13 H H13 N N N 0 5.754 3.02 5.841
56 H2 H H2 N N N 0 4.903 -0.603 3.125
57 H3 H H3 N N N 0 2.381 1.086 3.233
58 H4 H H4 N N N 0 2.741 0.046 5.491
59 H5 H H5 N N N 0 0.556 -1.505 4.028
60 H71 H 1H7 N N N 0 1.486 1.936 5.152
61 H72 H 2H7 N N N 0 0.502 1.393 6.499
62 H8 H H8 N N N 0 -1.166 2.856 4.575
63 H341 H 1H34 N N N 0 2.085 6.454 6.823
64 H342 H 2H34 N N N 0 0.826 6.675 5.593
65 H343 H 3H34 N N N 0 0.459 5.795 7.089
66 H331 H 1H33 N N N 0 -2.161 3.391 6.488
67 H332 H 2H33 N N N 0 -0.859 2.601 7.399
68 H333 H 3H33 N N N 0 -0.742 4.325 6.997
69 H351 H 1H35 N N N 0 3.682 5.979 6.909
70 H352 H 2H35 N N N 0 5.06 4.968 7.386
71 H353 H 3H35 N N N 0 5.291 6.296 6.232
72 HO12 H HO12 N N N 0 3.431 6.638 4.682
73 HO13 H HO13 N N N 0 6.123 4.694 4.74
74 H361 H 1H36 N N N 0 2.993 2.552 6.963
75 H362 H 2H36 N N N 0 4.388 3.155 7.862
76 H301 H 1H30 N N N 0 5.046 2.164 2.169
77 H302 H 2H30 N N N 0 5.552 0.657 1.382
78 H303 H 3H30 N N N 0 3.867 1.199 1.26
79 H321 H 1H32 N N N 0 -2.146 0.338 4.068
80 H322 H 2H32 N N N 0 -1.577 -0.901 5.204
81 H323 H 3H32 N N N 0 -1.853 0.759 5.767
82 H22 H H22 N N N 0 0.416 -3.051 5.042
83 H23 H H23 N N N 0 0.189 -2.815 8.105
84 H24 H H24 N N N 0 0.136 -5.4 6.451
85 H251 H 1H25 N N N 0 -2.274 -5.568 6.933
86 H252 H 2H25 N N N 0 -2.226 -4.071 7.876
87 H26 H H26 N N N 0 -1.656 -4.283 4.863
88 H271 H 1H27 N N N 0 -4.119 -4.315 6.02
89 H272 H 2H27 N N N 0 -3.828 -2.565 5.993
90 H273 H 3H27 N N N 0 -3.778 -3.497 4.483
91 HO8 H HO8 N N N 0 2.229 -2.692 7.141
92 H281 H 1H28 N N N 0 0.183 -4.354 10.31
93 H282 H 2H28 N N N 0 -1.356 -5.23 10.156
94 H283 H 3H28 N N N 0 -1.086 -3.74 9.227
95 H14 H H14 N N N 0 2.338 1.197 1.394
96 H151 H 1H15 N N N 0 2.966 0.596 -0.848
97 H152 H 2H15 N N N 0 4.093 -0.221 0.262
98 H17 H H17 N N N 0 0.95 -0.868 -1.829
99 H18 H H18 N N N 0 0.468 -1.923 1.017
100 HO6 H HO6 N N N 0 0.226 -3.243 -0.737
101 H201 H 1H20 N N N 0 4.687 -3.476 1.027
102 H202 H 2H20 N N N 0 4.688 -1.686 0.981
103 H203 H 3H20 N N N 0 4.979 -2.62 -0.51
104 H291 H 1H29 N N N 0 1.534 -6.487 9.415
105 H292 H 2H29 N N N 0 1.847 -4.759 9.14
106 H293 H 3H29 N N N 0 1.867 -5.893 7.773
107 H211 H 1H21 N N N 0 -1.501 -0.065 0.06
108 H212 H 2H21 N N N 0 -1.327 -1.362 -1.138
109 H213 H 3H21 N N N 0 -1.71 -1.758 0.548
110 H371 H 1H37 N N N 0 4.236 0.437 6.451
111 H372 H 2H37 N N N 0 5.633 1.041 7.352
112 H373 H 3H37 N N N 0 4.109 0.713 8.198
113 H311 H 1H31 N N N 0 3.857 -2.102 4.061
114 H312 H 2H31 N N N 0 3.621 -1.962 5.814
115 H313 H 3H31 N N N 0 2.383 -2.744 4.811
116 H191 H 1H19 N N N 0 3.271 -0.999 -2.754
117 H192 H 2H19 N N N 0 4.579 -1.702 -1.783
118 H193 H 3H19 N N N 0 3.298 -2.743 -2.434
119 H381 H 1H38 N N N 0 -1.427 -0.5 2.719
120 H382 H 2H38 N N N 0 0.274 -0.937 2.371
121 H383 H 3H38 N N N 0 -0.57 0.258 1.352



CTY : Chemical Bonds

Total Number of Bonds: 123
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 C11 C C sing 1.55 N N
2 C10 C9 C C sing 1.54 N N
3 C10 C34 C C sing 1.53 N N
4 C10 H10 C H sing 1.09 N N
5 C11 C12 C C sing 1.56 N N
6 C11 O12 C O sing 1.44 N N
7 C11 H11 C H sing 1.1 N N
8 C12 C13 C C sing 1.56 N N
9 C12 C35 C C sing 1.53 N N
10 C12 O13 C O sing 1.45 N N
11 C13 O2 C O sing 1.45 N N
12 C13 C36 C C sing 1.53 N N
13 C13 H13 C H sing 1.1 N N
14 O2 C1 O C sing 1.36 N N
15 C2 C3 C C sing 1.55 N N
16 C2 C1 C C sing 1.52 N N
17 C2 C30 C C sing 1.53 N N
18 C2 H2 C H sing 1.1 N N
19 C3 C4 C C sing 1.55 N N
20 C3 O3 C O sing 1.43 N N
21 C3 H3 C H sing 1.09 N N
22 C4 C5 C C sing 1.56 N N
23 C4 C31 C C sing 1.54 N N
24 C4 H4 C H sing 1.1 N N
25 C5 C6 C C sing 1.56 N N
26 C5 O7 C O sing 1.44 N N
27 C5 H5 C H sing 1.1 N N
28 C6 C7 C C sing 1.55 N N
29 C6 C32 C C sing 1.54 N N
30 C6 O10 C O sing 1.43 N N
31 C7 C8 C C sing 1.54 N N
32 C7 H71 C H sing 1.09 N N
33 C7 H72 C H sing 1.1 N N
34 C8 C9 C C sing 1.53 N N
35 C8 C33 C C sing 1.53 N N
36 C8 H8 C H sing 1.1 N N
37 C9 O11 C O doub 1.23 N N
38 C1 O1 C O doub 1.22 N N
39 O3 C14 O C sing 1.42 N N
40 O7 C22 O C sing 1.43 N N
41 C34 H341 C H sing 1.09 N N
42 C34 H342 C H sing 1.09 N N
43 C34 H343 C H sing 1.09 N N
44 C33 H331 C H sing 1.09 N N
45 C33 H332 C H sing 1.09 N N
46 C33 H333 C H sing 1.09 N N
47 C35 H351 C H sing 1.09 N N
48 C35 H352 C H sing 1.09 N N
49 C35 H353 C H sing 1.09 N N
50 O12 HO12 O H sing 0.97 N N
51 O13 HO13 O H sing 0.96 N N
52 C36 C37 C C sing 1.51 N N
53 C36 H361 C H sing 1.09 N N
54 C36 H362 C H sing 1.09 N N
55 C30 H301 C H sing 1.09 N N
56 C30 H302 C H sing 1.09 N N
57 C30 H303 C H sing 1.09 N N
58 C32 H321 C H sing 1.09 N N
59 C32 H322 C H sing 1.09 N N
60 C32 H323 C H sing 1.09 N N
61 O10 C38 O C sing 1.42 N N
62 C22 C23 C C sing 1.53 N N
63 C22 O9 C O sing 1.43 N N
64 C22 H22 C H sing 1.1 N N
65 C23 C24 C C sing 1.53 N N
66 C23 O8 C O sing 1.43 N N
67 C23 H23 C H sing 1.1 N N
68 C24 C25 C C sing 1.53 N N
69 C24 N1 C N sing 1.46 N N
70 C24 H24 C H sing 1.1 N N
71 C25 C26 C C sing 1.53 N N
72 C25 H251 C H sing 1.1 N N
73 C25 H252 C H sing 1.1 N N
74 C26 O9 C O sing 1.43 N N
75 C26 C27 C C sing 1.52 N N
76 C26 H26 C H sing 1.1 N N
77 N1 C28 N C sing 1.46 N N
78 N1 C29 N C sing 1.46 N N
79 C27 H271 C H sing 1.09 N N
80 C27 H272 C H sing 1.09 N N
81 C27 H273 C H sing 1.09 N N
82 O8 HO8 O H sing 0.97 N N
83 C28 H281 C H sing 1.09 N N
84 C28 H282 C H sing 1.09 N N
85 C28 H283 C H sing 1.09 N N
86 C14 C15 C C sing 1.53 N N
87 C14 O4 C O sing 1.43 N N
88 C14 H14 C H sing 1.09 N N
89 C15 C16 C C sing 1.54 N N
90 C15 H151 C H sing 1.1 N N
91 C15 H152 C H sing 1.1 N N
92 C16 C17 C C sing 1.54 N N
93 C16 O5 C O sing 1.43 N N
94 C16 C19 C C sing 1.53 N N
95 C17 C18 C C sing 1.53 N N
96 C17 O6 C O sing 1.42 N N
97 C17 H17 C H sing 1.1 N N
98 C18 O4 C O sing 1.43 N N
99 C18 C21 C C sing 1.53 N N
100 C18 H18 C H sing 1.1 N N
101 O5 C20 O C sing 1.42 N N
102 O6 HO6 O H sing 0.97 N N
103 C20 H201 C H sing 1.09 N N
104 C20 H202 C H sing 1.09 N N
105 C20 H203 C H sing 1.09 N N
106 C29 H291 C H sing 1.09 N N
107 C29 H292 C H sing 1.09 N N
108 C29 H293 C H sing 1.09 N N
109 C21 H211 C H sing 1.09 N N
110 C21 H212 C H sing 1.09 N N
111 C21 H213 C H sing 1.09 N N
112 C37 H371 C H sing 1.09 N N
113 C37 H372 C H sing 1.09 N N
114 C37 H373 C H sing 1.09 N N
115 C31 H311 C H sing 1.09 N N
116 C31 H312 C H sing 1.09 N N
117 C31 H313 C H sing 1.09 N N
118 C19 H191 C H sing 1.09 N N
119 C19 H192 C H sing 1.09 N N
120 C19 H193 C H sing 1.09 N N
121 C38 H381 C H sing 1.09 N N
122 C38 H382 C H sing 1.09 N N
123 C38 H383 C H sing 1.09 N N



CTY : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
CTY 1j5a Open in New Window Bound ligand 1 1
CTY 5igj Open in New Window Bound ligand 1 1
CTY 5igw Open in New Window Bound ligand 1 1
CTY 6u18 Open in New Window Bound ligand 2 1