Chemical Components in the PDB

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Z9Z : Summary

Code

Z9Z

One-letter code

X

Molecule name

pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate

Systematic names

ProgramVersionName
ACDLabs 12.01 pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate
OpenEye OEToolkits 1.7.6 pyridin-3-ylmethyl N-[(2R,5S)-5-[[(2R)-3-methyl-2-[[methyl-[(2-propan-2-yl-1,3-thiazol-4-yl)methyl]carbamoyl]amino]butanoyl]amino]-1,6-diphenyl-hexan-2-yl]carbamate

Formula

C39 H50 N6 O4 S

Formal charge

0

Molecular weight

698.917 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCc1cccnc1)NC(Cc2ccccc2)CCC(NC(=O)C(NC(=O)N(Cc3nc(sc3)C(C)C)C)C(C)C)Cc4ccccc4
SMILES CACTVS 3.370 CC(C)[CH](NC(=O)N(C)Cc1csc(n1)C(C)C)C(=O)N[CH](CC[CH](Cc2ccccc2)NC(=O)OCc3cccnc3)Cc4ccccc4
SMILES OpenEye OEToolkits 1.7.6 CC(C)c1nc(cs1)CN(C)C(=O)NC(C(C)C)C(=O)NC(CCC(Cc2ccccc2)NC(=O)OCc3cccnc3)Cc4ccccc4
Canonical SMILES CACTVS 3.370 CC(C)[C@@H](NC(=O)N(C)Cc1csc(n1)C(C)C)C(=O)N[C@@H](CC[C@H](Cc2ccccc2)NC(=O)OCc3cccnc3)Cc4ccccc4
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)c1nc(cs1)CN(C)C(=O)N[C@H](C(C)C)C(=O)N[C@@H](CC[C@H](Cc2ccccc2)NC(=O)OCc3cccnc3)Cc4ccccc4

IUPAC InChI

InChI=1S/C39H50N6O4S/c1-27(2)35(44-38(47)45(5)24-34-26-50-37(42-34)28(3)4)36(46)41-32(21-29-13-8-6-9-14-29)18-19-33(22-30-15-10-7-11-16-30)43-39(48)49-25-31-17-12-20-40-23-31/h6-17,20,23,26-28,32-33,35H,18-19,21-22,24-25H2,1-5H3,(H,41,46)(H,43,48)(H,44,47)/t32-,33+,35+/m0/s1

IUPAC InChI key

DXYIYKUZINROPB-VUHKNJSWSA-N
Z9Z

wwPDB Information

Atom count

100 (50 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-12-07

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



Z9Z : Atoms of Molecule

Total Number of Atoms: 100
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 -11.528 -1.664 0.247
2 C02 C C02 N N N 0 -10.126 -1.816 -0.347
3 C03 C C03 N N N 0 -9.542 -3.169 0.065
4 C04 C C04 N Y N 0 -9.241 -0.709 0.165
5 C06 C C06 N Y N 0 -7.907 1.068 0.034
6 C07 C C07 N N N 0 -7.158 2.145 -0.707
7 C09 C C09 N N N 0 -5.752 0.979 -2.468
8 C10 C C10 N N N 0 -4.783 1.727 -0.362
9 C13 C C13 R N N 0 -2.416 1.362 0.089
10 C14 C C14 N N N 0 -1.428 0.279 -0.261
11 C17 C C17 S N N 0 0.699 -0.863 0.069
12 C18 C C18 N N N 0 2.107 -0.416 0.468
13 C19 C C19 N N N 0 2.517 0.793 -0.375
14 C20 C C20 R N N 0 3.925 1.24 0.024
15 C21 C C21 N N N 0 4.286 2.522 -0.729
16 C22 C C22 N Y N 0 5.62 3.029 -0.247
17 C23 C C23 N Y N 0 5.681 3.915 0.812
18 C24 C C24 N Y N 0 6.905 4.375 1.26
19 C25 C C25 N Y N 0 8.068 3.959 0.64
20 C26 C C26 N Y N 0 8.007 3.077 -0.424
21 C27 C C27 N Y N 0 6.783 2.612 -0.867
22 C29 C C29 N N N 0 6.052 0.098 0.353
23 C32 C C32 N N N 0 8.166 -0.912 0.81
24 C33 C C33 N Y N 0 9.02 -2.056 0.328
25 C34 C C34 N Y N 0 8.904 -3.311 0.905
26 C35 C C35 N Y N 0 9.706 -4.335 0.426
27 C36 C C36 N Y N 0 10.597 -4.069 -0.597
28 C38 C C38 N Y N 0 9.934 -1.865 -0.691
29 C39 C C39 N N N 0 0.338 -2.145 0.822
30 C40 C C40 N Y N 0 -0.996 -2.652 0.339
31 C41 C C41 N Y N 0 -2.159 -2.24 0.963
32 C42 C C42 N Y N 0 -3.383 -2.7 0.516
33 C43 C C43 N Y N 0 -3.444 -3.582 -0.547
34 C44 C C44 N Y N 0 -2.281 -3.999 -1.167
35 C45 C C45 N Y N 0 -1.057 -3.534 -0.724
36 C46 C C46 N N N 0 -1.766 2.731 -0.117
37 C47 C C47 N N N 0 -2.724 3.827 0.355
38 C48 C C48 N N N 0 -1.456 2.93 -1.602
39 C49 C C49 N Y N 0 -7.872 0.947 1.365
40 H1 H H1 N N N 0 8.705 0.026 0.678
41 H10 H H10 N N N 0 3.522 3.277 -0.547
42 H11 H H11 N N N 0 6.736 1.923 -1.697
43 H12 H H12 N N N 0 8.916 2.752 -0.908
44 H13 H H13 N N N 0 9.025 4.322 0.986
45 H14 H H14 N N N 0 6.952 5.068 2.087
46 H15 H H15 N N N 0 4.772 4.241 1.297
47 H16 H H16 N N N 0 1.815 1.609 -0.205
48 H17 H H17 N N N 0 2.508 0.52 -1.431
49 H18 H H18 N N N 0 2.809 -1.233 0.298
50 H19 H H19 N N N 0 2.117 -0.143 1.523
51 H2 H H2 N N N 0 7.933 -1.052 1.866
52 H20 H H20 N N N 0 0.668 -1.051 -1.004
53 H21 H H21 N N N 0 1.102 -2.901 0.639
54 H22 H H22 N N N 0 0.283 -1.936 1.89
55 H23 H H23 N N N 0 -0.148 -3.86 -1.208
56 H24 H H24 N N N 0 -2.329 -4.688 -1.997
57 H25 H H25 N N N 0 -4.4 -3.945 -0.893
58 H26 H H26 N N N 0 -4.292 -2.374 1.0
59 H27 H H27 N N N 0 -2.111 -1.551 1.793
60 H28 H H28 N N N 0 -0.058 0.823 1.115
61 H29 H H29 N N N 0 -2.718 1.256 1.131
62 H3 H H3 N N N 0 10.034 -0.89 -1.143
63 H30 H H30 N N N 0 -0.841 2.785 0.457
64 H31 H H31 N N N 0 -2.381 2.876 -2.177
65 H32 H H32 N N N 0 -0.993 3.906 -1.75
66 H33 H H33 N N N 0 -0.774 2.15 -1.939
67 H34 H H34 N N N 0 -2.945 3.685 1.413
68 H35 H H35 N N N 0 -2.261 4.802 0.208
69 H36 H H36 N N N 0 -3.649 3.773 -0.22
70 H37 H H37 N N N 0 -3.518 0.82 -1.643
71 H38 H H38 N N N 0 -5.945 -0.089 -2.369
72 H39 H H39 N N N 0 -6.479 1.418 -3.151
73 H4 H H4 N N N 0 11.229 -4.861 -0.973
74 H40 H H40 N N N 0 -4.746 1.131 -2.861
75 H41 H H41 N N N 0 -6.995 2.995 -0.045
76 H42 H H42 N N N 0 -7.741 2.463 -1.571
77 H43 H H43 N N N 0 -7.324 1.581 2.046
78 H44 H H44 N N N 0 -10.184 -1.762 -1.434
79 H45 H H45 N N N 0 -9.484 -3.223 1.153
80 H46 H H46 N N N 0 -10.182 -3.969 -0.305
81 H47 H H47 N N N 0 -8.543 -3.277 -0.358
82 H48 H H48 N N N 0 -11.47 -1.718 1.334
83 H49 H H49 N N N 0 -11.944 -0.7 -0.047
84 H5 H H5 N N N 0 9.639 -5.327 0.848
85 H50 H H50 N N N 0 -12.168 -2.464 -0.123
86 H6 H H6 N N N 0 8.198 -3.489 1.704
87 H7 H H7 N N N 0 4.682 -0.446 -1.023
88 H8 H H8 N N N 0 3.956 1.427 1.097
89 H9 H H9 N N N 0 4.341 2.312 -1.798
90 N05 N N05 N Y N 0 -8.647 0.164 -0.577
91 N08 N N08 N N N 0 -5.866 1.62 -1.156
92 N12 N N12 N N N 0 -3.594 1.245 -0.775
93 N16 N N16 N N N 0 -0.261 0.19 0.409
94 N28 N N28 N N N 0 4.886 0.187 -0.316
95 N37 N N37 N Y N 0 10.685 -2.862 -1.118
96 O11 O O11 N N N 0 -4.878 2.26 0.728
97 O15 O O15 N N N 0 -1.682 -0.512 -1.144
98 O30 O O30 N N N 0 6.307 0.891 1.238
99 O31 O O31 N N N 0 6.933 -0.873 0.045
100 S50 S S50 N Y N 0 -8.876 -0.43 1.812



Z9Z : Chemical Bonds

Total Number of Bonds: 103
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N05 C06 N C sing 1.32 N Y
2 N05 C04 N C doub 1.29 N Y
3 C07 C06 C C sing 1.51 N N
4 C07 N08 C N sing 1.47 N N
5 C03 C02 C C sing 1.53 N N
6 C02 C04 C C sing 1.51 N N
7 C02 C01 C C sing 1.53 N N
8 C06 C49 C C doub 1.34 N Y
9 C04 S50 C S sing 1.71 N Y
10 C49 S50 C S sing 1.76 N Y
11 N08 C09 N C sing 1.46 N N
12 N08 C10 N C sing 1.35 N N
13 O11 C10 O C doub 1.22 N N
14 C10 N12 C N sing 1.35 N N
15 N12 C13 N C sing 1.47 N N
16 C42 C43 C C doub 1.38 N Y
17 C42 C41 C C sing 1.38 N Y
18 C35 C36 C C doub 1.38 N Y
19 C35 C34 C C sing 1.39 N Y
20 C36 N37 C N sing 1.32 N Y
21 C43 C44 C C sing 1.38 N Y
22 C13 C14 C C sing 1.51 N N
23 C13 C46 C C sing 1.53 N N
24 C41 C40 C C doub 1.38 N Y
25 C48 C46 C C sing 1.53 N N
26 C34 C33 C C doub 1.39 N Y
27 C14 O15 C O doub 1.21 N N
28 C14 N16 C N sing 1.35 N N
29 N37 C38 N C doub 1.32 N Y
30 C44 C45 C C doub 1.38 N Y
31 N16 C17 N C sing 1.46 N N
32 C46 C47 C C sing 1.53 N N
33 C40 C45 C C sing 1.38 N Y
34 C40 C39 C C sing 1.51 N N
35 C33 C38 C C sing 1.38 N Y
36 C33 C32 C C sing 1.51 N N
37 C17 C39 C C sing 1.53 N N
38 C17 C18 C C sing 1.53 N N
39 O31 C32 O C sing 1.45 N N
40 O31 C29 O C sing 1.35 N N
41 C18 C19 C C sing 1.53 N N
42 N28 C29 N C sing 1.35 N N
43 N28 C20 N C sing 1.47 N N
44 C29 O30 C O doub 1.22 N N
45 C20 C19 C C sing 1.53 N N
46 C20 C21 C C sing 1.53 N N
47 C24 C23 C C doub 1.38 N Y
48 C24 C25 C C sing 1.38 N Y
49 C23 C22 C C sing 1.38 N Y
50 C25 C26 C C doub 1.38 N Y
51 C22 C21 C C sing 1.51 N N
52 C22 C27 C C doub 1.38 N Y
53 C26 C27 C C sing 1.38 N Y
54 C32 H1 C H sing 1.09 N N
55 C32 H2 C H sing 1.09 N N
56 C38 H3 C H sing 1.08 N N
57 C36 H4 C H sing 1.08 N N
58 C35 H5 C H sing 1.08 N N
59 C34 H6 C H sing 1.08 N N
60 N28 H7 N H sing 0.97 N N
61 C20 H8 C H sing 1.09 N N
62 C21 H9 C H sing 1.09 N N
63 C21 H10 C H sing 1.09 N N
64 C27 H11 C H sing 1.08 N N
65 C26 H12 C H sing 1.08 N N
66 C25 H13 C H sing 1.08 N N
67 C24 H14 C H sing 1.08 N N
68 C23 H15 C H sing 1.08 N N
69 C19 H16 C H sing 1.09 N N
70 C19 H17 C H sing 1.09 N N
71 C18 H18 C H sing 1.09 N N
72 C18 H19 C H sing 1.09 N N
73 C17 H20 C H sing 1.09 N N
74 C39 H21 C H sing 1.09 N N
75 C39 H22 C H sing 1.09 N N
76 C45 H23 C H sing 1.08 N N
77 C44 H24 C H sing 1.08 N N
78 C43 H25 C H sing 1.08 N N
79 C42 H26 C H sing 1.08 N N
80 C41 H27 C H sing 1.08 N N
81 N16 H28 N H sing 0.97 N N
82 C13 H29 C H sing 1.09 N N
83 C46 H30 C H sing 1.09 N N
84 C48 H31 C H sing 1.09 N N
85 C48 H32 C H sing 1.09 N N
86 C48 H33 C H sing 1.09 N N
87 C47 H34 C H sing 1.09 N N
88 C47 H35 C H sing 1.09 N N
89 C47 H36 C H sing 1.09 N N
90 N12 H37 N H sing 0.97 N N
91 C09 H38 C H sing 1.09 N N
92 C09 H39 C H sing 1.09 N N
93 C09 H40 C H sing 1.09 N N
94 C07 H41 C H sing 1.09 N N
95 C07 H42 C H sing 1.09 N N
96 C49 H43 C H sing 1.08 N N
97 C02 H44 C H sing 1.09 N N
98 C03 H45 C H sing 1.09 N N
99 C03 H46 C H sing 1.09 N N
100 C03 H47 C H sing 1.09 N N
101 C01 H48 C H sing 1.09 N N
102 C01 H49 C H sing 1.09 N N
103 C01 H50 C H sing 1.09 N N



Z9Z : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Z9Z 4i4h Open in New Window Bound ligand 1 1