Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

GDM : Summary

Code

GDM

One-letter code

X

Molecule name

GELDANAMYCIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (4E,6Z,8S,9S,10E,12S,13R,14S,16R)-13-hydroxy-8,14,19-trimethoxy-4,10,12,16-tetramethyl-3,20,22-trioxo-2-azabicyclo[16.3.1]docosa-1(21),4,6,10,18-pentaen-9-yl carbamate
OpenEye OEToolkits 1.5.0 [(3R,5S,6R,7S,8E,10S,11S,12Z,14E)-6-hydroxy-5,11,21-trimethoxy-3,7,9,15-tetramethyl-16,20,22-trioxo-17-azabicyclo[16.3.1]docosa-1(21),8,12,14,18-pentaen-10-yl] carbamate

Formula

C29 H40 N2 O9

Formal charge

0

Molecular weight

560.636 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C(OC)=C2C(=O)C(=C1)NC(=O)C(=CC=CC(OC)C(OC(=O)N)C(=CC(C)C(O)C(OC)CC(C)C2)C)C
SMILES CACTVS 3.341 CO[CH]1C[CH](C)CC2=C(OC)C(=O)C=C(NC(=O)C(=CC=C[CH](OC)[CH](OC(N)=O)C(=C[CH](C)[CH]1O)C)C)C2=O
SMILES OpenEye OEToolkits 1.5.0 CC1CC(C(C(C=C(C(C(C=CC=C(C(=O)NC2=CC(=O)C(=C(C1)C2=O)OC)C)OC)OC(=O)N)C)C)O)OC
Canonical SMILES CACTVS 3.341 CO[C@H]1C[C@H](C)CC2=C(OC)C(=O)C=C(NC(=O)\C(=C\C=C/[C@H](OC)[C@@H](OC(N)=O)\C(=C\[C@H](C)[C@H]1O)C)C)C2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@H]1C[C@@H]([C@@H]([C@H](\C=C(\[C@@H]([C@H](\C=C/C=C(/C(=O)NC2=CC(=O)C(=C(C1)C2=O)OC)\C)OC)OC(=O)N)/C)C)O)OC

IUPAC InChI

InChI=1S/C29H40N2O9/c1-15-11-19-25(34)20(14-21(32)27(19)39-7)31-28(35)16(2)9-8-10-22(37-5)26(40-29(30)36)18(4)13-17(3)24(33)23(12-15)38-6/h8-10,13-15,17,22-24,26,33H,11-12H2,1-7H3,(H2,30,36)(H,31,35)/b10-8-,16-9+,18-13+/t15-,17+,22+,23+,24-,26+/m1/s1

IUPAC InChI key

QTQAWLPCGQOSGP-KSRBKZBZSA-N
GDM

wwPDB Information

Atom count

80 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



GDM : Atoms of Molecule

Total Number of Atoms: 80
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N 0 1.705 0.636 -1.266
2 O2 O O2 N N N 0 1.793 1.918 4.186
3 O3 O O3 N N N 0 0.583 0.045 5.545
4 O4 O O4 N N N 0 -0.223 -1.993 5.885
5 O5 O O5 N N N 0 -4.511 -1.193 0.882
6 O6 O O6 N N N 0 -1.518 0.718 0.011
7 O7 O O7 N N N 0 -1.147 -0.165 -6.473
8 O8 O O8 N N N 0 1.534 0.075 -7.103
9 O9 O O9 N N N 0 0.294 -1.032 -2.127
10 N1 N N1 N N N 0 2.972 -0.481 -2.662
11 N2 N N2 N N N 0 0.278 -0.809 7.694
12 C1 C C1 N N N 0 2.657 -0.107 -1.422
13 C2 C C2 N N N 0 3.358 -0.522 -0.215
14 C3 C C3 N N N 0 2.863 -0.088 0.967
15 C4 C C4 N N N 0 3.461 -0.42 2.25
16 C5 C C5 N N N 0 2.883 -0.052 3.397
17 C6 C C6 S N N 0 1.591 0.717 3.433
18 C7 C C7 S N N 0 0.495 -0.112 4.105
19 C8 C C8 N N N 0 -0.865 0.346 3.633
20 C9 C C9 N N N 0 -1.551 -0.419 2.826
21 C10 C C10 S N N 0 -2.913 -0.062 2.3
22 C11 C C11 R N N 0 -3.142 -0.791 0.968
23 C12 C C12 S N N 0 -2.814 0.152 -0.191
24 C13 C C13 N N N 0 -2.838 -0.635 -1.503
25 C14 C C14 R N N 0 -2.217 0.183 -2.633
26 C15 C C15 N N N 0 -1.927 -0.723 -3.835
27 C16 C C16 N N N 0 -0.489 -0.547 -4.256
28 C17 C C17 N N N 0 -0.175 -0.282 -5.541
29 C18 C C18 N N N 0 1.249 -0.121 -5.937
30 C19 C C19 N N N 0 2.305 -0.196 -4.927
31 C20 C C20 N N N 0 1.994 -0.431 -3.639
32 C21 C C21 N N N 0 0.577 -0.683 -3.256
33 C22 C C22 N N N 0 4.576 -1.397 -0.285
34 C23 C C23 N N N 0 2.211 2.922 3.259
35 C24 C C24 N N N 0 0.197 -0.956 6.357
36 C25 C C25 N N N 0 -1.404 1.671 4.106
37 C26 C C26 N N N 0 -3.986 -0.517 3.296
38 C27 C C27 N N N 0 -1.69 2.135 0.06
39 C28 C C28 N N N 0 -3.196 1.28 -3.064
40 C29 C C29 N N N 0 -1.151 1.199 -6.897
41 HO5 H HO5 N N N 0 -4.677 -1.782 1.63
42 HN1 H HN1 N N N 0 3.876 -0.78 -2.892
43 HN21 H 1HN2 N N N 0 0.0 -1.531 8.28
44 HN22 H 2HN2 N N N 0 0.614 0.018 8.072
45 H3 H H3 N N N 0 1.976 0.54 0.928
46 H4 H H4 N N N 0 4.393 -0.971 2.303
47 H5 H H5 N N N 0 3.367 -0.318 4.33
48 H6 H H6 N N N 0 1.276 0.98 2.428
49 H9 H H9 N N N 0 -1.11 -1.368 2.521
50 H7 H H7 N N N 0 0.629 -1.163 3.846
51 H10 H H10 N N N 0 -2.998 1.008 2.135
52 H11 H H11 N N N 0 -2.5 -1.668 0.921
53 H12 H H12 N N N 0 -3.558 0.947 -0.225
54 H131 H 1H13 N N N 0 -2.274 -1.561 -1.376
55 H132 H 2H13 N N N 0 -3.87 -0.879 -1.76
56 H14 H H14 N N N 0 -1.29 0.641 -2.295
57 H151 H 1H15 N N N 0 -2.103 -1.762 -3.555
58 H152 H 2H15 N N N 0 -2.591 -0.454 -4.657
59 H19 H H19 N N N 0 3.339 -0.065 -5.215
60 H221 H 1H22 N N N 0 4.944 -1.588 0.722
61 H222 H 2H22 N N N 0 4.317 -2.342 -0.763
62 H223 H 3H22 N N N 0 5.35 -0.897 -0.866
63 H231 H 1H23 N N N 0 2.378 3.86 3.789
64 H232 H 2H23 N N N 0 3.136 2.608 2.776
65 H233 H 3H23 N N N 0 1.437 3.064 2.504
66 H251 H 1H25 N N N 0 -2.389 1.839 3.67
67 H252 H 2H25 N N N 0 -1.485 1.664 5.193
68 H253 H 3H25 N N N 0 -0.729 2.469 3.797
69 H261 H 1H26 N N N 0 -3.827 -0.02 4.253
70 H262 H 2H26 N N N 0 -4.972 -0.256 2.911
71 H273 H 3H27 N N N 0 -2.432 2.385 0.818
72 H263 H 3H26 N N N 0 -3.922 -1.596 3.431
73 H271 H 1H27 N N N 0 -0.741 2.608 0.311
74 H272 H 2H27 N N N 0 -2.029 2.494 -0.911
75 H281 H 1H28 N N N 0 -2.754 1.865 -3.87
76 H282 H 2H28 N N N 0 -4.123 0.823 -3.411
77 H283 H 3H28 N N N 0 -3.407 1.931 -2.216
78 H291 H 1H29 N N N 0 -1.887 1.331 -7.689
79 H292 H 2H29 N N N 0 -1.405 1.84 -6.053
80 H293 H 3H29 N N N 0 -0.162 1.465 -7.271



GDM : Chemical Bonds

Total Number of Bonds: 81
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C1 O C doub 1.22 N N
2 O2 C6 O C sing 1.43 N N
3 O2 C23 O C sing 1.43 N N
4 O3 C7 O C sing 1.45 N N
5 O3 C24 O C sing 1.35 N N
6 O4 C24 O C doub 1.21 N N
7 O5 C11 O C sing 1.43 N N
8 O5 HO5 O H sing 0.97 N N
9 O6 C12 O C sing 1.43 N N
10 O6 C27 O C sing 1.43 N N
11 O7 C17 O C sing 1.35 N N
12 O7 C29 O C sing 1.43 N N
13 O8 C18 O C doub 1.22 N N
14 O9 C21 O C doub 1.22 N N
15 N1 C1 N C sing 1.33 N N
16 N1 C20 N C sing 1.38 N N
17 N1 HN1 N H sing 0.98 N N
18 N2 C24 N C sing 1.35 N N
19 N2 HN21 N H sing 0.97 N N
20 N2 HN22 N H sing 0.97 N N
21 C1 C2 C C sing 1.46 N N
22 C2 C3 C C doub 1.35 E N
23 C2 C22 C C sing 1.5 N N
24 C3 C4 C C sing 1.45 N N
25 C3 H3 C H sing 1.09 N N
26 C4 C5 C C doub 1.34 Z N
27 C4 H4 C H sing 1.08 N N
28 C5 C6 C C sing 1.5 N N
29 C5 H5 C H sing 1.08 N N
30 C6 C7 C C sing 1.53 N N
31 C6 H6 C H sing 1.09 N N
32 C7 C8 C C sing 1.51 N N
33 C7 H7 C H sing 1.09 N N
34 C8 C9 C C doub 1.31 E N
35 C8 C25 C C sing 1.51 N N
36 C9 C10 C C sing 1.5 N N
37 C9 H9 C H sing 1.09 N N
38 C10 C11 C C sing 1.54 N N
39 C10 C26 C C sing 1.53 N N
40 C10 H10 C H sing 1.09 N N
41 C11 C12 C C sing 1.53 N N
42 C11 H11 C H sing 1.09 N N
43 C12 C13 C C sing 1.53 N N
44 C12 H12 C H sing 1.09 N N
45 C13 C14 C C sing 1.53 N N
46 C13 H131 C H sing 1.09 N N
47 C13 H132 C H sing 1.09 N N
48 C14 C15 C C sing 1.53 N N
49 C14 C28 C C sing 1.53 N N
50 C14 H14 C H sing 1.09 N N
51 C15 C16 C C sing 1.51 N N
52 C15 H151 C H sing 1.09 N N
53 C15 H152 C H sing 1.09 N N
54 C16 C17 C C doub 1.35 N N
55 C16 C21 C C sing 1.47 N N
56 C17 C18 C C sing 1.49 N N
57 C18 C19 C C sing 1.46 N N
58 C19 C20 C C doub 1.35 N N
59 C19 H19 C H sing 1.08 N N
60 C20 C21 C C sing 1.49 N N
61 C22 H221 C H sing 1.09 N N
62 C22 H222 C H sing 1.09 N N
63 C22 H223 C H sing 1.09 N N
64 C23 H231 C H sing 1.09 N N
65 C23 H232 C H sing 1.09 N N
66 C23 H233 C H sing 1.09 N N
67 C25 H251 C H sing 1.09 N N
68 C25 H252 C H sing 1.09 N N
69 C25 H253 C H sing 1.09 N N
70 C26 H261 C H sing 1.09 N N
71 C26 H262 C H sing 1.09 N N
72 C26 H263 C H sing 1.09 N N
73 C27 H271 C H sing 1.09 N N
74 C27 H272 C H sing 1.09 N N
75 C27 H273 C H sing 1.09 N N
76 C28 H281 C H sing 1.09 N N
77 C28 H282 C H sing 1.09 N N
78 C28 H283 C H sing 1.09 N N
79 C29 H291 C H sing 1.09 N N
80 C29 H292 C H sing 1.09 N N
81 C29 H293 C H sing 1.09 N N



GDM : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
GDM 1a4h Open in New Window Bound ligand 1 1
GDM 1yet Open in New Window Bound ligand 1 1
GDM 2esa Open in New Window Bound ligand 1 1
GDM 2exl Open in New Window Bound ligand 2 1
GDM 2weq Open in New Window Bound ligand 1 1
GDM 2yga Open in New Window Bound ligand 1 1
GDM 2yge Open in New Window Bound ligand 1 1
GDM 2ygf Open in New Window Bound ligand 1 1
GDM 3c11 Open in New Window Bound ligand 1 1
GDM 4xdm Open in New Window Bound ligand 1 1