Chemical Components in the PDB

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83M : Summary

Code

83M

One-letter code

X

Molecule name

N-[(1R)-1-{(6S)-6-[(2-amino-2-oxoethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl}-2-(4-hydroxyphenyl)ethyl]-N~2~-tetradecanoyl-L-glutamine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(1R)-1-{(6S)-6-[(2-amino-2-oxoethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl}-2-(4-hydroxyphenyl)ethyl]-N~2~-tetradecanoyl-L-glutamine
OpenEye OEToolkits 2.0.6 (2~{S})-5-[[(1~{R})-1-[(6~{S})-6-[(2-azanyl-2-oxidanylidene-ethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl]-2-(4-hydroxyphenyl)ethyl]amino]-5-oxidanylidene-2-(tetradecanoylamino)pentanoic acid

Formula

C34 H54 N6 O7

Formal charge

0

Molecular weight

658.829 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(CCCCCCCC(NC(C(=O)O)CCC(=O)NC(Cc1ccc(O)cc1)C=2NC(C(NCC(N)=O)=O)CCN=2)=O)CCCCC
SMILES CACTVS 3.385 CCCCCCCCCCCCCC(=O)N[CH](CCC(=O)N[CH](Cc1ccc(O)cc1)C2=NCC[CH](N2)C(=O)NCC(N)=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 CCCCCCCCCCCCCC(=O)NC(CCC(=O)NC(Cc1ccc(cc1)O)C2=NCCC(N2)C(=O)NCC(=O)N)C(=O)O
Canonical SMILES CACTVS 3.385 CCCCCCCCCCCCCC(=O)N[C@@H](CCC(=O)N[C@H](Cc1ccc(O)cc1)C2=NCC[C@H](N2)C(=O)NCC(N)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CCCCCCCCCCCCCC(=O)N[C@@H](CCC(=O)N[C@H](Cc1ccc(cc1)O)C2=NCC[C@H](N2)C(=O)NCC(=O)N)C(=O)O

IUPAC InChI

InChI=1S/C34H54N6O7/c1-2-3-4-5-6-7-8-9-10-11-12-13-30(43)38-27(34(46)47)18-19-31(44)39-28(22-24-14-16-25(41)17-15-24)32-36-21-20-26(40-32)33(45)37-23-29(35)42/h14-17,26-28,41H,2-13,18-23H2,1H3,(H2,35,42)(H,36,40)(H,37,45)(H,38,43)(H,39,44)(H,46,47)/t26-,27-,28+/m0/s1

IUPAC InChI key

DGAYEIHJKULBKL-HZFUHODCSA-N
83M

wwPDB Information

Atom count

101 (47 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-12-21

Last modified at

2017-02-24

Status

Released

Obsoleted

Not Assigned



83M : Atoms of Molecule

Total Number of Atoms: 101
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C8 C C1 N N N 0 11.297 -1.619 0.211
2 C9 C C2 N N N 0 12.479 -1.237 1.104
3 C16 C C3 N N N 0 -0.035 1.82 -4.725
4 C6 C C4 N N N 0 8.974 -1.002 -0.473
5 C5 C C5 N N N 0 7.834 -0.004 -0.264
6 N23 N N1 N N N 0 0.9 1.596 -2.496
7 C1 C C6 N N N 0 3.189 1.23 -1.633
8 C2 C C7 N N N 0 4.329 0.231 -1.842
9 C3 C C8 N N N 0 5.511 0.613 -0.949
10 C4 C C9 N N N 0 6.652 -0.386 -1.158
11 C7 C C10 N N N 0 10.156 -0.62 0.42
12 C13 C C11 N N N 0 17.124 -2.47 2.473
13 C12 C C12 N N N 0 15.941 -2.852 1.58
14 C11 C C13 N N N 0 14.801 -1.854 1.788
15 C10 C C14 N N N 0 13.619 -2.236 0.895
16 C14 C C15 N N N 0 2.024 0.853 -2.513
17 C15 C C16 S N N 0 -0.232 1.23 -3.352
18 C17 C C17 R N N 0 -4.741 1.672 0.963
19 C18 C C18 N N N 0 -4.687 1.533 2.485
20 C19 C C19 N N N 0 -1.527 1.774 -2.744
21 C20 C C20 N N N 0 -1.791 1.083 -1.405
22 C21 C C21 N N N 0 -3.066 1.618 -0.806
23 C22 C C22 N N N 0 -5.914 0.891 0.428
24 C23 C C23 N Y N 0 -3.591 2.411 3.031
25 C24 C C24 N Y N 0 -3.868 3.717 3.391
26 C25 C C25 N Y N 0 -2.865 4.524 3.892
27 C26 C C26 N Y N 0 -1.579 4.024 4.034
28 C27 C C27 N Y N 0 -1.304 2.713 3.672
29 C28 C C28 N Y N 0 -2.312 1.908 3.177
30 C29 C C29 N N N 0 -7.049 -2.625 0.446
31 C32 C C30 N N N 0 -7.954 0.852 -0.872
32 C33 C C31 N N N 0 -7.767 -0.666 -0.921
33 C34 C C32 S N N 0 -7.281 -1.137 0.463
34 C35 C C33 N N N 0 -7.867 -4.918 0.551
35 C36 C C34 N N N 0 -9.185 -5.633 0.703
36 N24 N N2 N N N 0 -3.501 1.151 0.381
37 N30 N N3 N N N 0 -6.776 1.496 -0.302
38 N31 N N4 N N N 0 -6.014 -0.44 0.737
39 N32 N N5 N N N 0 -8.092 -3.471 0.568
40 N40 N N6 N N N 0 -9.224 -6.98 0.715
41 O15 O O1 N N N 0 2.099 -0.118 -3.236
42 O17 O O2 N N N 0 0.949 2.478 -4.964
43 O18 O O3 N N N 0 -0.954 1.614 -5.681
44 O22 O O4 N N N 0 -3.701 2.469 -1.393
45 O29 O O5 N N N 0 -0.59 4.816 4.526
46 O30 O O6 N N N 0 -5.925 -3.063 0.322
47 O39 O O7 N N N 0 -10.211 -4.996 0.814
48 H1 H H1 N N N 0 11.609 -1.6 -0.833
49 H2 H H2 N N N 0 10.954 -2.621 0.47
50 H3 H H3 N N N 0 12.821 -0.235 0.845
51 H4 H H4 N N N 0 12.166 -1.255 2.148
52 H5 H H5 N N N 0 8.632 -2.004 -0.214
53 H6 H H6 N N N 0 9.287 -0.984 -1.517
54 H7 H H7 N N N 0 7.521 -0.022 0.78
55 H8 H H8 N N N 0 8.176 0.998 -0.524
56 H9 H H9 N N N 0 0.84 2.373 -1.918
57 H10 H H10 N N N 0 2.876 1.211 -0.589
58 H11 H H11 N N N 0 3.531 2.231 -1.892
59 H12 H H12 N N N 0 3.987 -0.771 -1.583
60 H13 H H13 N N N 0 4.642 0.25 -2.886
61 H14 H H14 N N N 0 5.854 1.615 -1.208
62 H15 H H15 N N N 0 5.199 0.594 0.095
63 H19 H H19 N N N 0 10.499 0.382 0.161
64 H16 H H16 N N N 0 6.964 -0.367 -2.202
65 H17 H H17 N N N 0 6.309 -1.388 -0.899
66 H18 H H18 N N N 0 9.844 -0.639 1.464
67 H20 H H20 N N N 0 17.936 -3.182 2.324
68 H21 H H21 N N N 0 17.466 -1.468 2.214
69 H22 H H22 N N N 0 16.811 -2.489 3.517
70 H23 H H23 N N N 0 16.254 -2.834 0.536
71 H24 H H24 N N N 0 15.599 -3.854 1.839
72 H25 H H25 N N N 0 14.489 -1.872 2.833
73 H26 H H26 N N N 0 15.144 -0.852 1.53
74 H27 H H27 N N N 0 13.277 -3.237 1.155
75 H28 H H28 N N N 0 13.932 -2.217 -0.149
76 H29 H H29 N N N 0 -0.294 0.145 -3.428
77 H30 H H30 N N N 0 -4.854 2.723 0.697
78 H31 H H31 N N N 0 -5.643 1.837 2.912
79 H32 H H32 N N N 0 -4.486 0.495 2.749
80 H33 H H33 N N N 0 -1.431 2.848 -2.586
81 H34 H H34 N N N 0 -2.356 1.58 -3.423
82 H35 H H35 N N N 0 -1.887 0.009 -1.563
83 H36 H H36 N N N 0 -0.961 1.277 -0.725
84 H37 H H37 N N N 0 -4.869 4.107 3.28
85 H38 H H38 N N N 0 -3.082 5.545 4.173
86 H39 H H39 N N N 0 -0.304 2.321 3.781
87 H40 H H40 N N N 0 -2.099 0.886 2.9
88 H41 H H41 N N N 0 -8.113 1.228 -1.883
89 H42 H H42 N N N 0 -8.825 1.088 -0.261
90 H43 H H43 N N N 0 -8.717 -1.145 -1.158
91 H44 H H44 N N N 0 -7.027 -0.92 -1.68
92 H45 H H45 N N N 0 -8.022 -0.885 1.222
93 H46 H H46 N N N 0 -7.208 -5.193 1.374
94 H47 H H47 N N N 0 -7.406 -5.204 -0.395
95 H48 H H48 N N N 0 -2.994 0.471 0.85
96 H49 H H49 N N N 0 -5.264 -0.914 1.128
97 H50 H H50 N N N 0 -8.991 -3.121 0.666
98 H51 H H51 N N N 0 -8.403 -7.49 0.626
99 H52 H H52 N N N 0 -10.072 -7.44 0.813
100 H53 H H53 N N N 0 -0.784 2.012 -6.546
101 H54 H H54 N N N 0 -0.499 4.778 5.488



83M : Chemical Bonds

Total Number of Bonds: 102
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O39 C36 O C doub 1.21 N N
2 N40 C36 N C sing 1.35 N N
3 O30 C29 O C doub 1.21 N N
4 C36 C35 C C sing 1.51 N N
5 C29 N32 C N sing 1.35 N N
6 C29 C34 C C sing 1.51 N N
7 N32 C35 N C sing 1.46 N N
8 C32 C33 C C sing 1.53 N N
9 C32 N30 C N sing 1.46 N N
10 C18 C23 C C sing 1.51 N N
11 C18 C17 C C sing 1.53 N N
12 C33 C34 C C sing 1.54 N N
13 N30 C22 N C doub 1.28 N N
14 C28 C23 C C doub 1.38 N Y
15 C28 C27 C C sing 1.38 N Y
16 C34 N31 C N sing 1.47 N N
17 C23 C24 C C sing 1.38 N Y
18 C22 N31 C N sing 1.37 N N
19 C22 C17 C C sing 1.51 N N
20 C27 C26 C C doub 1.39 N Y
21 C17 N24 C N sing 1.47 N N
22 C24 C25 C C doub 1.38 N Y
23 N24 C21 N C sing 1.35 N N
24 C26 C25 C C sing 1.39 N Y
25 C26 O29 C O sing 1.36 N N
26 C21 O22 C O doub 1.21 N N
27 C21 C20 C C sing 1.51 N N
28 O17 C16 O C doub 1.21 N N
29 C20 C19 C C sing 1.53 N N
30 O18 C16 O C sing 1.34 N N
31 C16 C15 C C sing 1.51 N N
32 C19 C15 C C sing 1.53 N N
33 C15 N23 C N sing 1.47 N N
34 N23 C14 N C sing 1.35 N N
35 C14 O15 C O doub 1.21 N N
36 C14 C1 C C sing 1.51 N N
37 C1 C2 C C sing 1.53 N N
38 C2 C3 C C sing 1.53 N N
39 C3 C4 C C sing 1.53 N N
40 C4 C5 C C sing 1.53 N N
41 C5 C6 C C sing 1.53 N N
42 C6 C7 C C sing 1.53 N N
43 C8 C7 C C sing 1.53 N N
44 C8 C9 C C sing 1.53 N N
45 C10 C9 C C sing 1.53 N N
46 C10 C11 C C sing 1.53 N N
47 C12 C11 C C sing 1.53 N N
48 C12 C13 C C sing 1.53 N N
49 C8 H1 C H sing 1.09 N N
50 C8 H2 C H sing 1.09 N N
51 C9 H3 C H sing 1.09 N N
52 C9 H4 C H sing 1.09 N N
53 C6 H5 C H sing 1.09 N N
54 C6 H6 C H sing 1.09 N N
55 C5 H7 C H sing 1.09 N N
56 C5 H8 C H sing 1.09 N N
57 N23 H9 N H sing 0.97 N N
58 C1 H10 C H sing 1.09 N N
59 C1 H11 C H sing 1.09 N N
60 C2 H12 C H sing 1.09 N N
61 C2 H13 C H sing 1.09 N N
62 C3 H14 C H sing 1.09 N N
63 C3 H15 C H sing 1.09 N N
64 C4 H16 C H sing 1.09 N N
65 C4 H17 C H sing 1.09 N N
66 C7 H18 C H sing 1.09 N N
67 C7 H19 C H sing 1.09 N N
68 C13 H20 C H sing 1.09 N N
69 C13 H21 C H sing 1.09 N N
70 C13 H22 C H sing 1.09 N N
71 C12 H23 C H sing 1.09 N N
72 C12 H24 C H sing 1.09 N N
73 C11 H25 C H sing 1.09 N N
74 C11 H26 C H sing 1.09 N N
75 C10 H27 C H sing 1.09 N N
76 C10 H28 C H sing 1.09 N N
77 C15 H29 C H sing 1.09 N N
78 C17 H30 C H sing 1.09 N N
79 C18 H31 C H sing 1.09 N N
80 C18 H32 C H sing 1.09 N N
81 C19 H33 C H sing 1.09 N N
82 C19 H34 C H sing 1.09 N N
83 C20 H35 C H sing 1.09 N N
84 C20 H36 C H sing 1.09 N N
85 C24 H37 C H sing 1.08 N N
86 C25 H38 C H sing 1.08 N N
87 C27 H39 C H sing 1.08 N N
88 C28 H40 C H sing 1.08 N N
89 C32 H41 C H sing 1.09 N N
90 C32 H42 C H sing 1.09 N N
91 C33 H43 C H sing 1.09 N N
92 C33 H44 C H sing 1.09 N N
93 C34 H45 C H sing 1.09 N N
94 C35 H46 C H sing 1.09 N N
95 C35 H47 C H sing 1.09 N N
96 N24 H48 N H sing 0.97 N N
97 N31 H49 N H sing 0.97 N N
98 N32 H50 N H sing 0.97 N N
99 N40 H51 N H sing 0.97 N N
100 N40 H52 N H sing 0.97 N N
101 O18 H53 O H sing 0.97 N N
102 O29 H54 O H sing 0.97 N N



83M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
83M 5ubk Open in New Window Bound ligand 1 1