Chemical Components in the PDB

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0GM : Summary

Code

0GM

One-letter code

X

Molecule name

N-[(5S,9S,10S,13S)-9-hydroxy-5,10-bis(2-methylpropyl)-4,7,12,16-tetraoxo-3,6,11,17-tetraazabicyclo[17.3.1]tricosa-1(23),19,21-trien-13-yl]-3-(naphthalen-1-yl)-2-(naphthalen-1-ylmethyl)propanamide

Synonyms

CP-129,541

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(5S,9S,10S,13S)-9-hydroxy-5,10-bis(2-methylpropyl)-4,7,12,16-tetraoxo-3,6,11,17-tetraazabicyclo[17.3.1]tricosa-1(23),19,21-trien-13-yl]-3-(naphthalen-1-yl)-2-(naphthalen-1-ylmethyl)propanamide
OpenEye OEToolkits 1.7.0 N-[(7S,10S,11S,15S)-11-hydroxy-10,15-bis(2-methylpropyl)-4,8,13,16-tetraoxo-3,9,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-7-yl]-3-naphthalen-1-yl-2-(naphthalen-1-ylmethyl)propanamide

Formula

C51 H61 N5 O6

Formal charge

0

Molecular weight

840.06 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C6NC(C(O)CC(=O)NC(C(=O)NCc1cccc(c1)CNC(=O)CCC6NC(=O)C(Cc3c2ccccc2ccc3)Cc5c4ccccc4ccc5)CC(C)C)CC(C)C
SMILES CACTVS 3.370 CC(C)C[CH]1NC(=O)[CH](CCC(=O)NCc2cccc(CNC(=O)[CH](CC(C)C)NC(=O)C[CH]1O)c2)NC(=O)C(Cc3cccc4ccccc34)Cc5cccc6ccccc56
SMILES OpenEye OEToolkits 1.7.0 CC(C)CC1C(CC(=O)NC(C(=O)NCc2cccc(c2)CNC(=O)CCC(C(=O)N1)NC(=O)C(Cc3cccc4c3cccc4)Cc5cccc6c5cccc6)CC(C)C)O
Canonical SMILES CACTVS 3.370 CC(C)C[C@@H]1NC(=O)[C@H](CCC(=O)NCc2cccc(CNC(=O)[C@H](CC(C)C)NC(=O)C[C@@H]1O)c2)NC(=O)C(Cc3cccc4ccccc34)Cc5cccc6ccccc56
Canonical SMILES OpenEye OEToolkits 1.7.0 CC(C)C[C@H]1[C@H](CC(=O)N[C@H](C(=O)NCc2cccc(c2)CNC(=O)CC[C@@H](C(=O)N1)NC(=O)C(Cc3cccc4c3cccc4)Cc5cccc6c5cccc6)CC(C)C)O

IUPAC InChI

InChI=1S/C51H61N5O6/c1-32(2)24-44-46(57)29-48(59)54-45(25-33(3)4)50(61)53-31-35-13-9-12-34(26-35)30-52-47(58)23-22-43(51(62)56-44)55-49(60)40(27-38-18-10-16-36-14-5-7-20-41(36)38)28-39-19-11-17-37-15-6-8-21-42(37)39/h5-21,26,32-33,40,43-46,57H,22-25,27-31H2,1-4H3,(H,52,58)(H,53,61)(H,54,59)(H,55,60)(H,56,62)/t43-,44-,45-,46-/m0/s1

IUPAC InChI key

KFCMUWOMPCWWCH-AXYJRABVSA-N
0GM

wwPDB Information

Atom count

123 (62 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-09-14

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



0GM : Atoms of Molecule

Total Number of Atoms: 123
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 2.775 0.434 -0.806
2 O O O N N N 0 2.23 0.972 -1.747
3 CA C CA N N N 0 4.276 0.302 -0.78
4 CB1 C CB1 N N N 0 4.85 0.737 -2.129
5 C1A C C1A N Y N 0 6.336 0.489 -2.146
6 C2A C C2A N Y N 0 7.2 1.491 -1.824
7 C3A C C3A N Y N 0 8.578 1.281 -1.835
8 C4A C C4A N Y N 0 9.1 0.07 -2.173
9 C11 C C11 N Y N 0 8.239 -0.99 -2.505
10 C5A C C5A N Y N 0 8.741 -2.255 -2.854
11 C6A C C6A N Y N 0 7.877 -3.256 -3.176
12 C7A C C7A N Y N 0 6.499 -3.047 -3.166
13 C8A C C8A N Y N 0 5.977 -1.835 -2.833
14 C12 C C12 N Y N 0 6.838 -0.776 -2.494
15 CB2 C CB2 N N N 0 4.846 1.19 0.327
16 C1B C C1B N Y N 0 4.394 0.673 1.669
17 C2B C C2B N Y N 0 3.338 1.251 2.304
18 C3B C C3B N Y N 0 2.907 0.788 3.545
19 C4B C C4B N Y N 0 3.532 -0.253 4.161
20 C13 C C13 N Y N 0 4.622 -0.878 3.533
21 C5B C C5B N Y N 0 5.29 -1.959 4.136
22 C6B C C6B N Y N 0 6.346 -2.536 3.501
23 C7B C C7B N Y N 0 6.778 -2.072 2.259
24 C8B C C8B N Y N 0 6.156 -1.029 1.646
25 C14 C C14 N Y N 0 5.062 -0.407 2.271
26 N N N N N N 0 2.038 -0.046 0.215
27 CA1 C CA1 S N N 0 0.575 -0.024 0.136
28 C1 C C1 N N N 0 0.062 1.287 0.674
29 O1 O O1 N N N 0 0.326 1.632 1.807
30 CB C CB N N N 0 0.003 -1.176 0.965
31 CG C CG N N N 0 -0.604 -2.224 0.031
32 CD C CD N N N 0 -1.488 -3.152 0.824
33 OE1 O OE1 N N N 0 -1.118 -3.588 1.893
34 N1 N N1 N N N 0 -0.705 2.076 -0.127
35 CA2 C CA2 S N N 0 -1.18 3.344 0.462
36 CB3 C CB3 N N N 0 -0.095 4.414 0.32
37 CG1 C CG1 N N N 0 -0.531 5.683 1.054
38 CD1 C CD1 N N N 0 -0.611 5.402 2.556
39 CD2 C CD2 N N N 0 0.487 6.796 0.798
40 CH C CH S N N 0 -2.442 3.793 -0.278
41 OH O OH N N N 0 -2.557 3.07 -1.505
42 CM C CM N N N 0 -3.669 3.516 0.594
43 C2 C C2 N N N 0 -4.606 2.593 -0.14
44 O2 O O2 N N N 0 -4.2 1.892 -1.042
45 N2 N N2 N N N 0 -5.923 2.558 0.228
46 CA3 C CA3 S N N 0 -6.765 1.629 -0.561
47 C3 C C3 N N N 0 -7.088 0.425 0.285
48 O3 O O3 N N N 0 -7.293 0.544 1.474
49 CB4 C CB4 N N N 0 -6.005 1.187 -1.813
50 CG2 C CG2 N N N 0 -6.979 0.536 -2.798
51 CD3 C CD3 N N N 0 -7.947 1.594 -3.331
52 CD4 C CD4 N N N 0 -6.197 -0.072 -3.963
53 N3 N N3 N N N 0 -7.148 -0.801 -0.312
54 CA4 C CA4 N N N 0 -7.786 -1.854 0.514
55 CG3 C CG3 N Y N 0 -6.988 -3.121 0.362
56 CD5 C CD5 N Y N 0 -5.677 -3.174 0.797
57 CD6 C CD6 N Y N 0 -7.572 -4.239 -0.207
58 CE1 C CE1 N Y N 0 -4.953 -4.345 0.67
59 CE2 C CE2 N Y N 0 -6.848 -5.409 -0.334
60 CZ C CZ N Y N 0 -5.538 -5.462 0.105
61 CB5 C CB5 N N N 0 -3.526 -4.404 1.15
62 N4 N N4 N N N 0 -2.707 -3.493 0.323
63 HA H HA N N N 0 4.545 -0.737 -0.588
64 HB1 H HB1 N N N 0 4.377 0.164 -2.927
65 HB1A H HB1A N N N 0 4.657 1.799 -2.281
66 H2A H H2A N N N 0 6.812 2.463 -1.557
67 H3A H H3A N N N 0 9.241 2.093 -1.576
68 H4A H H4A N N N 0 10.17 -0.078 -2.177
69 H5A H H5A N N N 0 9.806 -2.432 -2.867
70 H6A H H6A N N N 0 8.265 -4.228 -3.444
71 H7A H H7A N N N 0 5.835 -3.858 -3.426
72 H8A H H8A N N N 0 4.907 -1.687 -2.829
73 HB2 H HB2 N N N 0 5.935 1.175 0.28
74 HB2A H HB2A N N N 0 4.491 2.212 0.193
75 H2B H H2B N N N 0 2.827 2.081 1.839
76 H3B H H3B N N N 0 2.066 1.264 4.028
77 H4B H H4B N N N 0 3.186 -0.602 5.123
78 H5B H H5B N N N 0 4.967 -2.329 5.097
79 H6B H H6B N N N 0 6.858 -3.366 3.966
80 H7B H H7B N N N 0 7.62 -2.547 1.777
81 H8B H H8B N N N 0 6.502 -0.68 0.684
82 HN H HN N N N 0 2.476 -0.402 1.004
83 HA1 H HA1 N N N 0 0.265 -0.136 -0.903
84 HB H HB N N N 0 -0.77 -0.794 1.633
85 HBA H HBA N N N 0 0.799 -1.631 1.554
86 HG H HG N N N 0 -1.195 -1.727 -0.738
87 HGA H HGA N N N 0 0.195 -2.798 -0.439
88 HB3 H HB3 N N N 0 0.836 4.046 0.751
89 HN1 H HN1 N N N 0 -0.927 1.82 -1.036
90 HA2 H HA2 N N N 0 -1.41 3.193 1.517
91 HB3A H HB3A N N N 0 0.057 4.639 -0.736
92 HG1 H HG1 N N N 0 -1.51 5.996 0.691
93 HD1 H HD1 N N N 0 -0.831 6.327 3.088
94 HD1A H HD1A N N N 0 -1.401 4.676 2.748
95 HD1B H HD1B N N N 0 0.342 5.001 2.902
96 HD2 H HD2 N N N 0 0.544 6.997 -0.272
97 HD2A H HD2A N N N 0 0.177 7.7 1.321
98 HD2B H HD2B N N N 0 1.466 6.484 1.161
99 HH H HH N N N 0 -2.379 4.86 -0.489
100 HOH H HOH N N N 0 -3.271 3.38 -2.079
101 HM H HM N N N 0 -4.179 4.454 0.812
102 HMA H HMA N N N 0 -3.354 3.048 1.527
103 HN2 H HN2 N N N 0 -6.278 3.1 0.95
104 HA3 H HA3 N N N 0 -7.688 2.131 -0.851
105 HB4 H HB4 N N N 0 -5.54 2.054 -2.282
106 HB4A H HB4A N N N 0 -5.235 0.467 -1.536
107 H17 H H17 N N N 0 -7.541 -0.247 -2.289
108 HD3 H HD3 N N N 0 -7.393 2.337 -3.905
109 HD3A H HD3A N N N 0 -8.689 1.118 -3.973
110 H13 H H13 N N N 0 -8.449 2.082 -2.496
111 HD4 H HD4 N N N 0 -5.507 -0.826 -3.583
112 HD4A H HD4A N N N 0 -6.891 -0.536 -4.664
113 HD4B H HD4B N N N 0 -5.635 0.711 -4.472
114 HN3 H HN3 N N N 0 -6.799 -0.957 -1.203
115 HA4 H HA4 N N N 0 -7.801 -1.539 1.558
116 HA4A H HA4A N N N 0 -8.806 -2.019 0.169
117 HD5 H HD5 N N N 0 -5.219 -2.3 1.236
118 HD6 H HD6 N N N 0 -8.595 -4.196 -0.551
119 HE2 H HE2 N N N 0 -7.305 -6.281 -0.778
120 HZ H HZ N N N 0 -4.972 -6.377 0.007
121 HB5 H HB5 N N N 0 -3.149 -5.422 1.052
122 HB5A H HB5A N N N 0 -3.477 -4.092 2.193
123 HN4 H HN4 N N N 0 -3.022 -3.156 -0.53



0GM : Chemical Bonds

Total Number of Bonds: 128
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA1 N C sing 1.47 N N
2 C1 N1 C N sing 1.36 N N
3 C1 O1 C O doub 1.21 N N
4 N2 CA3 N C sing 1.48 N N
5 C3 N3 C N sing 1.36 N N
6 C3 CA3 C C sing 1.51 N N
7 O3 C3 O C doub 1.21 N N
8 CB CA1 C C sing 1.53 N N
9 CD CG C C sing 1.51 N N
10 CD N4 C N sing 1.36 N N
11 CG CB C C sing 1.53 N N
12 CA1 C1 C C sing 1.51 N N
13 CA3 CB4 C C sing 1.53 N N
14 CB4 CG2 C C sing 1.53 N N
15 OE1 CD O C doub 1.21 N N
16 CG2 CD3 C C sing 1.53 N N
17 CG2 CD4 C C sing 1.53 N N
18 C N C N sing 1.35 N N
19 C CA C C sing 1.51 N N
20 O C O C doub 1.21 N N
21 N1 CA2 N C sing 1.48 N N
22 C2 N2 C N sing 1.37 N N
23 O2 C2 O C doub 1.21 N N
24 N4 CB5 N C sing 1.48 N N
25 CA CB1 C C sing 1.53 N N
26 OH CH O C sing 1.43 N N
27 CM C2 C C sing 1.51 N N
28 CM CH C C sing 1.53 N N
29 CZ CE1 C C doub 1.38 N Y
30 CZ CE2 C C sing 1.38 N Y
31 C11 C12 C C sing 1.42 N Y
32 C11 C5A C C sing 1.41 N Y
33 C12 C8A C C sing 1.41 N Y
34 C13 C5B C C sing 1.41 N Y
35 C13 C14 C C sing 1.42 N Y
36 C14 C8B C C sing 1.41 N Y
37 C1A C12 C C doub 1.4 N Y
38 C1A CB1 C C sing 1.51 N N
39 C1B C14 C C doub 1.41 N Y
40 C1B CB2 C C sing 1.51 N N
41 C2A C1A C C sing 1.36 N Y
42 C2B C1B C C sing 1.36 N Y
43 C3A C2A C C doub 1.39 N Y
44 C3A C4A C C sing 1.36 N Y
45 C3B C2B C C doub 1.39 N Y
46 C3B C4B C C sing 1.36 N Y
47 C4A C11 C C doub 1.41 N Y
48 C4B C13 C C doub 1.4 N Y
49 C5A C6A C C doub 1.36 N Y
50 C5B C6B C C doub 1.36 N Y
51 C6A C7A C C sing 1.39 N Y
52 C6B C7B C C sing 1.39 N Y
53 C8A C7A C C doub 1.36 N Y
54 C8B C7B C C doub 1.36 N Y
55 CA2 CH C C sing 1.53 N N
56 CA2 CB3 C C sing 1.53 N N
57 CA4 N3 C N sing 1.48 N N
58 CB2 CA C C sing 1.53 N N
59 CB5 CE1 C C sing 1.51 N N
60 CD5 CG3 C C doub 1.38 N Y
61 CD6 CG3 C C sing 1.38 N Y
62 CE1 CD5 C C sing 1.38 N Y
63 CE2 CD6 C C doub 1.38 N Y
64 CG1 CB3 C C sing 1.53 N N
65 CG1 CD1 C C sing 1.53 N N
66 CG1 CD2 C C sing 1.53 N N
67 CG3 CA4 C C sing 1.51 N N
68 N HN N H sing 0.97 N N
69 N2 HN2 N H sing 0.97 N N
70 CB HB C H sing 1.09 N N
71 CB HBA C H sing 1.09 N N
72 CG HG C H sing 1.09 N N
73 CG HGA C H sing 1.09 N N
74 CA1 HA1 C H sing 1.09 N N
75 CA3 HA3 C H sing 1.09 N N
76 CB4 HB4 C H sing 1.09 N N
77 CB4 HB4A C H sing 1.09 N N
78 CD3 HD3 C H sing 1.09 N N
79 CD3 HD3A C H sing 1.09 N N
80 CD3 H13 C H sing 1.09 N N
81 CD4 HD4 C H sing 1.09 N N
82 CD4 HD4A C H sing 1.09 N N
83 CD4 HD4B C H sing 1.09 N N
84 CG2 H17 C H sing 1.09 N N
85 N1 HN1 N H sing 0.97 N N
86 N3 HN3 N H sing 0.97 N N
87 N4 HN4 N H sing 0.97 N N
88 CA HA C H sing 1.09 N N
89 CH HH C H sing 1.09 N N
90 OH HOH O H sing 0.97 N N
91 CM HM C H sing 1.09 N N
92 CM HMA C H sing 1.09 N N
93 CZ HZ C H sing 1.08 N N
94 C2A H2A C H sing 1.08 N N
95 C2B H2B C H sing 1.08 N N
96 C3A H3A C H sing 1.08 N N
97 C3B H3B C H sing 1.08 N N
98 C4A H4A C H sing 1.08 N N
99 C4B H4B C H sing 1.08 N N
100 C5A H5A C H sing 1.08 N N
101 C5B H5B C H sing 1.08 N N
102 C6A H6A C H sing 1.08 N N
103 C6B H6B C H sing 1.08 N N
104 C7A H7A C H sing 1.08 N N
105 C7B H7B C H sing 1.08 N N
106 C8A H8A C H sing 1.08 N N
107 C8B H8B C H sing 1.08 N N
108 CA2 HA2 C H sing 1.09 N N
109 CA4 HA4 C H sing 1.09 N N
110 CA4 HA4A C H sing 1.09 N N
111 CB1 HB1 C H sing 1.09 N N
112 CB1 HB1A C H sing 1.09 N N
113 CB2 HB2 C H sing 1.09 N N
114 CB2 HB2A C H sing 1.09 N N
115 CB3 HB3 C H sing 1.09 N N
116 CB3 HB3A C H sing 1.09 N N
117 CB5 HB5 C H sing 1.09 N N
118 CB5 HB5A C H sing 1.09 N N
119 CD1 HD1 C H sing 1.09 N N
120 CD1 HD1A C H sing 1.09 N N
121 CD1 HD1B C H sing 1.09 N N
122 CD2 HD2 C H sing 1.09 N N
123 CD2 HD2A C H sing 1.09 N N
124 CD2 HD2B C H sing 1.09 N N
125 CD5 HD5 C H sing 1.08 N N
126 CD6 HD6 C H sing 1.08 N N
127 CE2 HE2 C H sing 1.08 N N
128 CG1 HG1 C H sing 1.09 N N



0GM : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
0GM 1fq5 Open in New Window Bound ligand 1 1
0GM 1gvv Open in New Window Bound ligand 1 1