Chemical Components in the PDB

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079 : Summary

Code

079

One-letter code

X

Molecule name

(S)-N-((2S,3S,4R,5R)-4-amino-3,5-dihydroxy-1,6-diphenylhexan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 4-amino-1,2,4,6-tetradeoxy-2-{[N-(phenoxyacetyl)-L-valyl]amino}-1,6-diphenyl-D-glucitol
OpenEye OEToolkits 1.7.2 (2S)-N-[(2S,3S,4R,5R)-4-azanyl-3,5-bis(oxidanyl)-1,6-diphenyl-hexan-2-yl]-3-methyl-2-(2-phenoxyethanoylamino)butanamide

Formula

C31 H39 N3 O5

Formal charge

0

Molecular weight

533.658 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC(Cc1ccccc1)C(O)C(N)C(O)Cc2ccccc2)C(NC(=O)COc3ccccc3)C(C)C
SMILES CACTVS 3.370 CC(C)[CH](NC(=O)COc1ccccc1)C(=O)N[CH](Cc2ccccc2)[CH](O)[CH](N)[CH](O)Cc3ccccc3
SMILES OpenEye OEToolkits 1.7.2 CC(C)C(C(=O)NC(Cc1ccccc1)C(C(C(Cc2ccccc2)O)N)O)NC(=O)COc3ccccc3
Canonical SMILES CACTVS 3.370 CC(C)[C@H](NC(=O)COc1ccccc1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](O)[C@H](N)[C@H](O)Cc3ccccc3
Canonical SMILES OpenEye OEToolkits 1.7.2 CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)[C@H]([C@@H]([C@@H](Cc2ccccc2)O)N)O)NC(=O)COc3ccccc3

IUPAC InChI

InChI=1S/C31H39N3O5/c1-21(2)29(34-27(36)20-39-24-16-10-5-11-17-24)31(38)33-25(18-22-12-6-3-7-13-22)30(37)28(32)26(35)19-23-14-8-4-9-15-23/h3-17,21,25-26,28-30,35,37H,18-20,32H2,1-2H3,(H,33,38)(H,34,36)/t25-,26+,28+,29-,30+/m0/s1

IUPAC InChI key

ASWZRLFSSZUWDR-UZMSACSVSA-N

Has sub-components

06Y , 078
079

wwPDB Information

Atom count

78 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

PEPTIDE-LIKE

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-09-19

Last modified at

2012-08-10

Status

Released

Obsoleted

Not Assigned



079 : Atoms of Molecule

Total Number of Atoms: 78
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 4.193 1.051 0.375
2 O1 O O1 N N N 0 4.239 1.585 1.462
3 C2 C C2 N N N 0 5.462 0.584 -0.29
4 O2 O O2 N N N 0 6.578 0.881 0.552
5 C3 C C3 N Y N 0 7.807 0.523 0.096
6 C4 C C4 N Y N 0 8.935 0.781 0.862
7 C5 C C5 N Y N 0 10.183 0.416 0.396
8 C6 C C6 N Y N 0 10.309 -0.207 -0.831
9 C7 C C7 N Y N 0 9.187 -0.466 -1.597
10 C8 C C8 N Y N 0 7.936 -0.108 -1.133
11 N1 N N1 N N N 0 3.006 0.869 -0.236
12 C9 C C9 S N N 0 1.771 1.317 0.413
13 C13 C C13 N N N 0 0.61 0.507 -0.103
14 O3 O O3 N N N 0 0.655 0.021 -1.213
15 C10 C C10 N N N 0 1.539 2.797 0.101
16 C11 C C11 N N N 0 1.305 2.971 -1.401
17 C12 C C12 N N N 0 0.314 3.295 0.87
18 C27 C C27 N Y N 0 -8.216 0.791 -1.378
19 C28 C C28 N Y N 0 -9.412 1.475 -1.265
20 C29 C C29 N Y N 0 -10.203 1.303 -0.145
21 C30 C C30 N Y N 0 -9.798 0.447 0.863
22 C31 C C31 N Y N 0 -8.602 -0.237 0.749
23 C26 C C26 N Y N 0 -7.811 -0.065 -0.371
24 C25 C C25 N N N 0 -6.51 -0.815 -0.498
25 C24 C C24 R N N 0 -5.379 0.02 0.107
26 O5 O O5 N N N 0 -5.595 0.168 1.512
27 C23 C C23 R N N 0 -4.042 -0.684 -0.132
28 N3 N N3 N N N 0 -3.82 -0.836 -1.576
29 C22 C C22 S N N 0 -2.911 0.151 0.473
30 O4 O O4 N N N 0 -2.908 1.45 -0.122
31 C14 C C14 S N N 0 -1.57 -0.536 0.205
32 C15 C C15 N N N 0 -1.522 -1.87 0.953
33 C16 C C16 N Y N 0 -0.256 -2.603 0.592
34 C17 C C17 N Y N 0 -0.24 -3.466 -0.487
35 C18 C C18 N Y N 0 0.922 -4.138 -0.818
36 N2 N N2 N N N 0 -0.479 0.324 0.67
37 C19 C C19 N Y N 0 2.068 -3.947 -0.069
38 C20 C C20 N Y N 0 2.052 -3.083 1.01
39 C21 C C21 N Y N 0 0.892 -2.408 1.338
40 H34 H H34 N N N 0 5.41 -0.492 -0.458
41 H35 H H35 N N N 0 5.581 1.095 -1.245
42 H36 H H36 N N N 0 8.837 1.268 1.821
43 H37 H H37 N N N 0 11.061 0.617 0.992
44 H38 H H38 N N N 0 11.286 -0.492 -1.194
45 H39 H H39 N N N 0 9.288 -0.952 -2.556
46 H40 H H40 N N N 0 7.06 -0.31 -1.732
47 H33 H H33 N N N 0 2.968 0.441 -1.106
48 H25 H H25 N N N 0 1.858 1.183 1.491
49 H26 H H26 N N N 0 2.415 3.373 0.401
50 H30 H H30 N N N 0 0.429 2.395 -1.701
51 H31 H H31 N N N 0 1.14 4.026 -1.623
52 H32 H H32 N N N 0 2.178 2.617 -1.949
53 H27 H H27 N N N 0 0.472 3.149 1.939
54 H28 H H28 N N N 0 0.163 4.355 0.666
55 H29 H H29 N N N 0 -0.566 2.735 0.553
56 H1 H H1 N N N 0 -7.6 0.922 -2.256
57 H2 H H2 N N N 0 -9.728 2.143 -2.052
58 H3 H H3 N N N 0 -11.137 1.837 -0.056
59 H4 H H4 N N N 0 -10.415 0.313 1.738
60 H5 H H5 N N N 0 -8.285 -0.906 1.536
61 H6 H H6 N N N 0 -6.585 -1.764 0.033
62 H7 H H7 N N N 0 -6.3 -1.003 -1.551
63 H8 H H8 N N N 0 -5.361 1.003 -0.364
64 H9 H H9 N N N 0 -5.622 -0.669 1.996
65 H10 H H10 N N N 0 -4.059 -1.667 0.338
66 H11 H H11 N N N 0 -3.697 0.062 -2.02
67 H12 H H12 N N N 0 -3.033 -1.441 -1.759
68 H14 H H14 N N N 0 -3.063 0.244 1.548
69 H15 H H15 N N N 0 -2.777 1.444 -1.08
70 H16 H H16 N N N 0 -1.461 -0.716 -0.865
71 H17 H H17 N N N 0 -1.542 -1.686 2.027
72 H18 H H18 N N N 0 -2.385 -2.475 0.672
73 H19 H H19 N N N 0 -1.136 -3.615 -1.072
74 H20 H H20 N N N 0 0.934 -4.813 -1.661
75 H21 H H21 N N N 0 2.975 -4.473 -0.327
76 H22 H H22 N N N 0 2.948 -2.934 1.595
77 H23 H H23 N N N 0 0.881 -1.73 2.179
78 H24 H H24 N N N 0 -0.541 0.761 1.533



079 : Chemical Bonds

Total Number of Bonds: 80
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C29 C28 C C doub 1.38 N Y
2 C29 C30 C C sing 1.38 N Y
3 C28 C27 C C sing 1.38 N Y
4 C30 C31 C C doub 1.38 N Y
5 C27 C26 C C doub 1.38 N Y
6 C31 C26 C C sing 1.38 N Y
7 C26 C25 C C sing 1.51 N N
8 O5 C24 O C sing 1.43 N N
9 C25 C24 C C sing 1.53 N N
10 C24 C23 C C sing 1.53 N N
11 C23 N3 C N sing 1.47 N N
12 C23 C22 C C sing 1.53 N N
13 C22 C14 C C sing 1.53 N N
14 C22 O4 C O sing 1.43 N N
15 O3 C13 O C doub 1.21 N N
16 C14 C15 C C sing 1.53 N N
17 C14 N2 C N sing 1.46 N N
18 C17 C18 C C doub 1.38 N Y
19 C17 C16 C C sing 1.38 N Y
20 C12 C10 C C sing 1.53 N N
21 C13 N2 C N sing 1.35 N N
22 C13 C9 C C sing 1.51 N N
23 C15 C16 C C sing 1.51 N N
24 C18 C19 C C sing 1.38 N Y
25 C16 C21 C C doub 1.38 N Y
26 C10 C9 C C sing 1.53 N N
27 C10 C11 C C sing 1.53 N N
28 C9 N1 C N sing 1.47 N N
29 C19 C20 C C doub 1.38 N Y
30 N1 C1 N C sing 1.35 N N
31 C21 C20 C C sing 1.38 N Y
32 C8 C7 C C doub 1.38 N Y
33 C8 C3 C C sing 1.39 N Y
34 C7 C6 C C sing 1.38 N Y
35 O2 C3 O C sing 1.36 N N
36 O2 C2 O C sing 1.43 N N
37 C3 C4 C C doub 1.39 N Y
38 C1 O1 C O doub 1.21 N N
39 C1 C2 C C sing 1.51 N N
40 C6 C5 C C doub 1.38 N Y
41 C4 C5 C C sing 1.38 N Y
42 C27 H1 C H sing 1.08 N N
43 C28 H2 C H sing 1.08 N N
44 C29 H3 C H sing 1.08 N N
45 C30 H4 C H sing 1.08 N N
46 C31 H5 C H sing 1.08 N N
47 C25 H6 C H sing 1.09 N N
48 C25 H7 C H sing 1.09 N N
49 C24 H8 C H sing 1.09 N N
50 O5 H9 O H sing 0.97 N N
51 C23 H10 C H sing 1.09 N N
52 N3 H11 N H sing 1.01 N N
53 N3 H12 N H sing 1.01 N N
54 C22 H14 C H sing 1.09 N N
55 O4 H15 O H sing 0.97 N N
56 C14 H16 C H sing 1.09 N N
57 C15 H17 C H sing 1.09 N N
58 C15 H18 C H sing 1.09 N N
59 C17 H19 C H sing 1.08 N N
60 C18 H20 C H sing 1.08 N N
61 C19 H21 C H sing 1.08 N N
62 C20 H22 C H sing 1.08 N N
63 C21 H23 C H sing 1.08 N N
64 N2 H24 N H sing 0.97 N N
65 C9 H25 C H sing 1.09 N N
66 C10 H26 C H sing 1.09 N N
67 C12 H27 C H sing 1.09 N N
68 C12 H28 C H sing 1.09 N N
69 C12 H29 C H sing 1.09 N N
70 C11 H30 C H sing 1.09 N N
71 C11 H31 C H sing 1.09 N N
72 C11 H32 C H sing 1.09 N N
73 N1 H33 N H sing 0.97 N N
74 C2 H34 C H sing 1.09 N N
75 C2 H35 C H sing 1.09 N N
76 C4 H36 C H sing 1.08 N N
77 C5 H37 C H sing 1.08 N N
78 C6 H38 C H sing 1.08 N N
79 C7 H39 C H sing 1.08 N N
80 C8 H40 C H sing 1.08 N N



079 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
079 3tog Open in New Window Bound ligand 2 1
079 3toh Open in New Window Bound ligand 1 1