Chemical Components in the PDB

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XLI : Summary

Code

XLI

One-letter code

X

Molecule name

N-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide
OpenEye OEToolkits 1.7.0 (2R,4S,5S)-5-[[(2S)-2-[[(2S)-2-acetamido-4-methyl-pentanoyl]amino]-4-methylsulfanyl-butanoyl]amino]-N-butyl-4-hydroxy-2,7-dimethyl-octanamide

Formula

C27 H52 N4 O5 S

Formal charge

0

Molecular weight

544.791 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC(C(=O)NC(CC(C)C)C(O)CC(C(=O)NCCCC)C)CCSC)C(NC(=O)C)CC(C)C
SMILES CACTVS 3.370 CCCCNC(=O)[CH](C)C[CH](O)[CH](CC(C)C)NC(=O)[CH](CCSC)NC(=O)[CH](CC(C)C)NC(C)=O
SMILES OpenEye OEToolkits 1.7.0 CCCCNC(=O)C(C)CC(C(CC(C)C)NC(=O)C(CCSC)NC(=O)C(CC(C)C)NC(=O)C)O
Canonical SMILES CACTVS 3.370 CCCCNC(=O)[C@H](C)C[C@H](O)[C@H](CC(C)C)NC(=O)[C@H](CCSC)NC(=O)[C@H](CC(C)C)NC(C)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 CCCCNC(=O)[C@H](C)C[C@@H]([C@H](CC(C)C)NC(=O)[C@H](CCSC)NC(=O)[C@H](CC(C)C)NC(=O)C)O

IUPAC InChI

InChI=1S/C27H52N4O5S/c1-9-10-12-28-25(34)19(6)16-24(33)22(14-17(2)3)31-26(35)21(11-13-37-8)30-27(36)23(15-18(4)5)29-20(7)32/h17-19,21-24,33H,9-16H2,1-8H3,(H,28,34)(H,29,32)(H,30,36)(H,31,35)/t19-,21+,22+,23+,24+/m1/s1

IUPAC InChI key

PEWRQHFGBBTOMS-FFYZIMEISA-N

Has sub-components

ACE , LEU , MET , 1OL , LYT
XLI

wwPDB Information

Atom count

89 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-01-04

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



XLI : Atoms of Molecule

Total Number of Atoms: 89
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 7.013 0.592 0.643
2 O O O N N N 0 6.509 -0.076 1.52
3 CH3 C CH3 N N N 0 8.208 1.458 0.948
4 N N N N N N 0 6.509 0.556 -0.607
5 CA C CA S N N 0 5.351 -0.29 -0.904
6 C1 C C1 N N N 0 4.183 0.137 -0.053
7 O1 O O1 N N N 0 4.373 0.783 0.956
8 CB C CB N N N 0 5.694 -1.75 -0.602
9 CG C CG N N N 0 6.796 -2.222 -1.553
10 CD1 C CD1 N N N 0 7.227 -3.639 -1.171
11 CD2 C CD2 N N N 0 6.266 -2.22 -2.989
12 N1 N N1 N N N 0 2.928 -0.198 -0.412
13 CA1 C CA1 S N N 0 1.793 0.218 0.416
14 C2 C C2 N N N 0 0.641 -0.728 0.2
15 O2 O O2 N N N 0 0.756 -1.658 -0.569
16 CB1 C CB1 N N N 0 1.37 1.636 0.026
17 CG1 C CG1 N N N 0 2.496 2.615 0.362
18 SD S SD N N N 0 1.994 4.296 -0.101
19 CE C CE N N N 0 3.434 5.295 0.366
20 N2 N N2 N N N 0 -0.518 -0.541 0.863
21 CA2 C CA2 S N N 0 -1.674 -1.393 0.572
22 C3 C C3 S N N 0 -2.963 -0.609 0.83
23 O3 O O3 N N N 0 -3.005 -0.199 2.198
24 CB2 C CB2 N N N 0 -1.638 -2.627 1.476
25 CG2 C CG2 N N N 0 -2.771 -3.577 1.087
26 CD11 C CD11 N N N 0 -2.523 -4.117 -0.323
27 CD21 C CD21 N N N 0 -2.823 -4.742 2.078
28 CM C CM N N N 0 -2.999 0.625 -0.074
29 CA3 C CA3 R N N 0 -4.318 1.37 0.134
30 CB3 C CB3 N N N 0 -4.285 2.691 -0.639
31 C4 C C4 N N N 0 -5.459 0.523 -0.368
32 O4 O O4 N N N 0 -5.238 -0.57 -0.845
33 C11 C C11 N N N 0 -7.833 0.155 -0.776
34 N3 N N3 N N N 0 -6.724 0.979 -0.287
35 C21 C C21 N N N 0 -9.153 0.901 -0.568
36 C31 C C31 N N N 0 -10.31 0.041 -1.078
37 C41 C C41 N N N 0 -11.63 0.786 -0.87
38 H1 H H1 N N N 0 9.122 0.886 0.786
39 H2 H H2 N N N 0 8.204 2.328 0.291
40 H3 H H3 N N N 0 8.163 1.787 1.986
41 H H H N N N 0 6.912 1.09 -1.308
42 HA H HA N N N 0 5.088 -0.19 -1.957
43 HB2 H HB2 N N N 0 6.042 -1.836 0.427
44 HB3 H HB3 N N N 0 4.807 -2.368 -0.739
45 HG H HG N N N 0 7.651 -1.55 -1.481
46 HD11 H HD11 N N N 0 6.372 -4.312 -1.243
47 HD12 H HD12 N N N 0 8.012 -3.976 -1.849
48 HD13 H HD13 N N N 0 7.605 -3.641 -0.148
49 HD21 H HD21 N N N 0 7.051 -2.556 -3.666
50 HD22 H HD22 N N N 0 5.411 -2.892 -3.061
51 HD23 H HD23 N N N 0 5.959 -1.211 -3.261
52 H4 H H4 N N N 0 2.776 -0.714 -1.219
53 HA1 H HA1 N N N 0 2.085 0.202 1.467
54 HB21 H HB21 N N N 0 1.164 1.672 -1.043
55 HB31 H HB31 N N N 0 0.472 1.911 0.579
56 HG2 H HG2 N N N 0 2.703 2.579 1.431
57 HG3 H HG3 N N N 0 3.394 2.339 -0.191
58 HE1 H HE1 N N N 0 3.617 5.192 1.435
59 HE2 H HE2 N N N 0 4.309 4.952 -0.187
60 HE3 H HE3 N N N 0 3.243 6.342 0.129
61 H5 H H5 N N N 0 -0.587 0.158 1.532
62 HA2 H HA2 N N N 0 -1.641 -1.706 -0.471
63 HB22 H HB22 N N N 0 -0.681 -3.135 1.359
64 HB32 H HB32 N N N 0 -1.761 -2.32 2.515
65 HG1 H HG1 N N N 0 -3.72 -3.04 1.108
66 HD14 H HD14 N N N 0 -1.618 -4.725 -0.324
67 HD15 H HD15 N N N 0 -3.371 -4.728 -0.633
68 HD16 H HD16 N N N 0 -2.402 -3.284 -1.015
69 HD24 H HD24 N N N 0 -3.0 -4.357 3.082
70 HD25 H HD25 N N N 0 -3.631 -5.42 1.8
71 HD26 H HD26 N N N 0 -1.875 -5.279 2.056
72 H51 H H51 N N N 0 -3.823 -1.243 0.614
73 H52 H H52 N N N 0 -2.268 0.369 2.462
74 HM2 H HM2 N N N 0 -2.166 1.283 0.176
75 HM3 H HM3 N N N 0 -2.917 0.315 -1.115
76 HA3 H HA3 N N N 0 -4.457 1.574 1.196
77 HB1 H HB1 N N N 0 -5.187 3.262 -0.421
78 HB23 H HB23 N N N 0 -3.409 3.266 -0.339
79 HB33 H HB33 N N N 0 -4.236 2.484 -1.708
80 H11 H H11 N N N 0 -7.694 -0.048 -1.837
81 H12 H H12 N N N 0 -7.857 -0.785 -0.225
82 HN2 H HN2 N N N 0 -6.901 1.854 0.094
83 H21 H H21 N N N 0 -9.292 1.105 0.494
84 H22 H H22 N N N 0 -9.129 1.842 -1.118
85 H31 H H31 N N N 0 -10.171 -0.163 -2.139
86 H32 H H32 N N N 0 -10.334 -0.9 -0.527
87 H41 H H41 N N N 0 -12.455 0.174 -1.234
88 H42 H H42 N N N 0 -11.769 0.99 0.191
89 H43 H H43 N N N 0 -11.606 1.727 -1.421



XLI : Chemical Bonds

Total Number of Bonds: 88
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C O C O doub 1.21 N N
2 C CH3 C C sing 1.51 N N
3 C N C N sing 1.35 N N
4 CH3 H1 C H sing 1.09 N N
5 CH3 H2 C H sing 1.09 N N
6 CH3 H3 C H sing 1.09 N N
7 N CA N C sing 1.46 N N
8 N H N H sing 0.97 N N
9 CA C1 C C sing 1.51 N N
10 CA CB C C sing 1.53 N N
11 CA HA C H sing 1.09 N N
12 C1 O1 C O doub 1.21 N N
13 C1 N1 C N sing 1.35 N N
14 CB CG C C sing 1.53 N N
15 CB HB2 C H sing 1.09 N N
16 CB HB3 C H sing 1.09 N N
17 CG CD1 C C sing 1.53 N N
18 CG CD2 C C sing 1.53 N N
19 CG HG C H sing 1.09 N N
20 CD1 HD11 C H sing 1.09 N N
21 CD1 HD12 C H sing 1.09 N N
22 CD1 HD13 C H sing 1.09 N N
23 CD2 HD21 C H sing 1.09 N N
24 CD2 HD22 C H sing 1.09 N N
25 CD2 HD23 C H sing 1.09 N N
26 N1 CA1 N C sing 1.47 N N
27 N1 H4 N H sing 0.97 N N
28 CA1 C2 C C sing 1.51 N N
29 CA1 CB1 C C sing 1.53 N N
30 CA1 HA1 C H sing 1.09 N N
31 C2 O2 C O doub 1.21 N N
32 C2 N2 C N sing 1.35 N N
33 CB1 CG1 C C sing 1.53 N N
34 CB1 HB21 C H sing 1.09 N N
35 CB1 HB31 C H sing 1.09 N N
36 CG1 SD C S sing 1.81 N N
37 CG1 HG2 C H sing 1.09 N N
38 CG1 HG3 C H sing 1.09 N N
39 SD CE S C sing 1.81 N N
40 CE HE1 C H sing 1.09 N N
41 CE HE2 C H sing 1.09 N N
42 CE HE3 C H sing 1.09 N N
43 N2 CA2 N C sing 1.47 N N
44 N2 H5 N H sing 0.97 N N
45 CA2 C3 C C sing 1.53 N N
46 CA2 CB2 C C sing 1.53 N N
47 CA2 HA2 C H sing 1.09 N N
48 C3 O3 C O sing 1.43 N N
49 C3 CM C C sing 1.53 N N
50 CB2 CG2 C C sing 1.53 N N
51 CB2 HB22 C H sing 1.09 N N
52 CB2 HB32 C H sing 1.09 N N
53 CG2 CD11 C C sing 1.53 N N
54 CG2 CD21 C C sing 1.53 N N
55 CG2 HG1 C H sing 1.09 N N
56 CD11 HD14 C H sing 1.09 N N
57 CD11 HD15 C H sing 1.09 N N
58 CD11 HD16 C H sing 1.09 N N
59 CD21 HD24 C H sing 1.09 N N
60 CD21 HD25 C H sing 1.09 N N
61 CD21 HD26 C H sing 1.09 N N
62 CM CA3 C C sing 1.53 N N
63 CM HM2 C H sing 1.09 N N
64 CM HM3 C H sing 1.09 N N
65 CA3 CB3 C C sing 1.53 N N
66 CA3 C4 C C sing 1.51 N N
67 CA3 HA3 C H sing 1.09 N N
68 CB3 HB1 C H sing 1.09 N N
69 CB3 HB23 C H sing 1.09 N N
70 CB3 HB33 C H sing 1.09 N N
71 C4 O4 C O doub 1.21 N N
72 C4 N3 C N sing 1.35 N N
73 C11 N3 C N sing 1.47 N N
74 C11 C21 C C sing 1.53 N N
75 C11 H11 C H sing 1.09 N N
76 C11 H12 C H sing 1.09 N N
77 N3 HN2 N H sing 0.97 N N
78 C21 C31 C C sing 1.53 N N
79 C21 H21 C H sing 1.09 N N
80 C21 H22 C H sing 1.09 N N
81 C31 C41 C C sing 1.53 N N
82 C31 H31 C H sing 1.09 N N
83 C31 H32 C H sing 1.09 N N
84 C41 H41 C H sing 1.09 N N
85 C41 H42 C H sing 1.09 N N
86 C41 H43 C H sing 1.09 N N
87 C3 H51 C H sing 1.09 N N
88 O3 H52 O H sing 0.97 N N



XLI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XLI 3k5d Open in New Window Bound ligand 3 1