Chemical Components in the PDB

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JJ1 : Summary

Code

JJ1

One-letter code

X

Molecule name

N-[(1S)-1-{[(1S)-5-AMINO-1-[(2-CYCLOHEXYLETHYL)CARBAMOYL]PENTYL]CARBAMOYL}-2-HYDROXYETHYL]-10-HYDROXYDECANAMIDE

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(10-hydroxydecanoyl)-L-seryl-N-(2-cyclohexylethyl)-L-lysinamide
OpenEye OEToolkits 1.9.2 N-[(2S)-1-[[(2S)-6-azanyl-1-(2-cyclohexylethylamino)-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-10-oxidanyl-decanamide

Formula

C27 H52 N4 O5

Formal charge

0

Molecular weight

512.726 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC(C(=O)NC(C(=O)NCCC1CCCCC1)CCCCN)CO)CCCCCCCCCO
SMILES CACTVS 3.385 NCCCC[CH](NC(=O)[CH](CO)NC(=O)CCCCCCCCCO)C(=O)NCCC1CCCCC1
SMILES OpenEye OEToolkits 1.9.2 C1CCC(CC1)CCNC(=O)C(CCCCN)NC(=O)C(CO)NC(=O)CCCCCCCCCO
Canonical SMILES CACTVS 3.385 NCCCC[C@H](NC(=O)[C@H](CO)NC(=O)CCCCCCCCCO)C(=O)NCCC1CCCCC1
Canonical SMILES OpenEye OEToolkits 1.9.2 C1CCC(CC1)CCNC(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)CCCCCCCCCO

IUPAC InChI

InChI=1S/C27H52N4O5/c28-18-11-10-15-23(26(35)29-19-17-22-13-7-6-8-14-22)31-27(36)24(21-33)30-25(34)16-9-4-2-1-3-5-12-20-32/h22-24,32-33H,1-21,28H2,(H,29,35)(H,30,34)(H,31,36)/t23-,24-/m0/s1

IUPAC InChI key

WOFDCVFMMXKBIZ-ZEQRLZLVSA-N
JJ1

wwPDB Information

Atom count

88 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-09-20

Last modified at

2014-09-19

Status

Released

Obsoleted

Not Assigned



JJ1 : Atoms of Molecule

Total Number of Atoms: 88
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O4 O O4 N N N 0 0.638 -0.449 1.12
2 C6 C C6 N N N 0 0.78 0.186 0.096
3 N1 N N1 N N N 0 1.99 0.25 -0.494
4 C1 C C1 S N N 0 3.133 -0.447 0.101
5 C2 C C2 N N N 0 3.144 -1.903 -0.369
6 C3 C C3 N N N 0 1.906 -2.622 0.171
7 C4 C C4 N N N 0 1.917 -4.078 -0.299
8 C5 C C5 N N N 0 0.679 -4.797 0.24
9 N N N N N N 0 0.689 -6.195 -0.211
10 C C C N N N 0 4.411 0.229 -0.326
11 N3 N N3 N N N 0 5.598 -0.243 0.103
12 C19 C C19 N N N 0 6.84 0.413 -0.313
13 C20 C C20 N N N 0 8.034 -0.314 0.309
14 C21 C C21 N N N 0 9.332 0.371 -0.125
15 C26 C C26 N N N 0 10.529 -0.428 0.393
16 C25 C C25 N N N 0 11.826 0.257 -0.04
17 C24 C C24 N N N 0 11.871 1.674 0.535
18 C23 C C23 N N N 0 10.674 2.474 0.017
19 C22 C C22 N N N 0 9.377 1.788 0.451
20 O O O N N N 0 4.371 1.197 -1.056
21 C7 C C7 S N N 0 -0.397 0.897 -0.519
22 C8 C C8 N N N 0 -0.106 2.398 -0.591
23 O1 O O1 N N N 0 0.234 2.88 0.711
24 N2 N N2 N N N 0 -1.589 0.67 0.302
25 C9 C C9 N N N 0 -2.815 0.751 -0.253
26 O3 O O3 N N N 0 -2.931 1.011 -1.432
27 C10 C C10 N N N 0 -4.041 0.517 0.592
28 C11 C C11 N N N 0 -5.293 0.666 -0.275
29 C12 C C12 N N N 0 -6.538 0.428 0.583
30 C13 C C13 N N N 0 -7.79 0.578 -0.283
31 C14 C C14 N N N 0 -9.035 0.34 0.574
32 C15 C C15 N N N 0 -10.287 0.49 -0.292
33 C16 C C16 N N N 0 -11.531 0.252 0.565
34 C17 C C17 N N N 0 -12.784 0.402 -0.301
35 C18 C C18 N N N 0 -14.028 0.164 0.556
36 O2 O O2 N N N 0 -15.198 0.304 -0.253
37 H1 H H1 N N N 0 2.104 0.758 -1.313
38 H7 H H7 N N N 0 -0.57 0.512 -1.524
39 HA H HA N N N 0 3.052 -0.416 1.188
40 H21C H H21C N N N 0 3.136 -1.933 -1.458
41 H22C H H22C N N N 0 4.042 -2.397 0.002
42 H31C H H31C N N N 0 1.914 -2.592 1.26
43 H32C H H32C N N N 0 1.008 -2.127 -0.2
44 H41C H H41C N N N 0 1.909 -4.108 -1.389
45 H42C H H42C N N N 0 2.815 -4.573 0.071
46 H51C H H51C N N N 0 0.687 -4.767 1.33
47 H52C H H52C N N N 0 -0.219 -4.302 -0.13
48 HN1 H HN1 N N N 0 -0.119 -6.692 0.132
49 HN2 H HN2 N N N 0 0.747 -6.25 -1.217
50 H3 H H3 N N N 0 5.631 -1.017 0.686
51 H191 H H191 N N N 0 6.922 0.383 -1.399
52 H192 H H192 N N N 0 6.833 1.451 0.022
53 H201 H H201 N N N 0 7.953 -0.284 1.395
54 H202 H H202 N N N 0 8.042 -1.352 -0.026
55 H221 H H221 N N N 0 8.524 2.358 0.082
56 H21 H H21 N N N 0 9.371 0.42 -1.213
57 H261 H H261 N N N 0 10.49 -0.477 1.482
58 H262 H H262 N N N 0 10.497 -1.438 -0.017
59 H222 H H222 N N N 0 9.338 1.74 1.539
60 H251 H H251 N N N 0 12.679 -0.312 0.329
61 H252 H H252 N N N 0 11.865 0.306 -1.129
62 H241 H H241 N N N 0 11.832 1.626 1.623
63 H242 H H242 N N N 0 12.795 2.163 0.226
64 H231 H H231 N N N 0 10.706 3.483 0.427
65 H232 H H232 N N N 0 10.713 2.522 -1.071
66 H81C H H81C N N N 0 0.726 2.574 -1.273
67 H82C H H82C N N N 0 -0.99 2.923 -0.953
68 H2 H H2 N N N 0 -1.496 0.462 1.245
69 HB H HB N N N 0 0.432 3.826 0.741
70 H101 H H101 N N N 0 -4.007 -0.489 1.011
71 H102 H H102 N N N 0 -4.069 1.247 1.401
72 H111 H H111 N N N 0 -5.327 1.672 -0.694
73 H112 H H112 N N N 0 -5.264 -0.064 -1.084
74 H121 H H121 N N N 0 -6.504 -0.577 1.002
75 H122 H H122 N N N 0 -6.566 1.158 1.392
76 H131 H H131 N N N 0 -7.824 1.584 -0.703
77 H132 H H132 N N N 0 -7.761 -0.152 -1.092
78 H141 H H141 N N N 0 -9.0 -0.665 0.993
79 H142 H H142 N N N 0 -9.063 1.071 1.383
80 H151 H H151 N N N 0 -10.321 1.495 -0.711
81 H152 H H152 N N N 0 -10.258 -0.24 -1.101
82 H161 H H161 N N N 0 -11.497 -0.753 0.984
83 H162 H H162 N N N 0 -11.56 0.982 1.374
84 H171 H H171 N N N 0 -12.818 1.407 -0.72
85 H172 H H172 N N N 0 -12.755 -0.328 -1.11
86 H181 H H181 N N N 0 -13.994 -0.841 0.975
87 H182 H H182 N N N 0 -14.057 0.894 1.365
88 HC H HC N N N 0 -16.026 0.166 0.226



JJ1 : 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 O4 C6 O C doub 1.21 N N
2 C6 N1 C N sing 1.35 N N
3 C6 C7 C C sing 1.51 N N
4 N1 C1 N C sing 1.47 N N
5 C1 C2 C C sing 1.53 N N
6 C1 C C C sing 1.51 N N
7 C2 C3 C C sing 1.53 N N
8 C3 C4 C C sing 1.53 N N
9 C4 C5 C C sing 1.53 N N
10 C5 N C N sing 1.47 N N
11 C N3 C N sing 1.35 N N
12 C O C O doub 1.21 N N
13 N3 C19 N C sing 1.46 N N
14 C19 C20 C C sing 1.53 N N
15 C20 C21 C C sing 1.53 N N
16 C21 C26 C C sing 1.53 N N
17 C21 C22 C C sing 1.53 N N
18 C26 C25 C C sing 1.53 N N
19 C25 C24 C C sing 1.53 N N
20 C24 C23 C C sing 1.53 N N
21 C23 C22 C C sing 1.53 N N
22 C7 C8 C C sing 1.53 N N
23 C7 N2 C N sing 1.47 N N
24 C8 O1 C O sing 1.43 N N
25 N2 C9 N C sing 1.35 N N
26 C9 O3 C O doub 1.21 N N
27 C9 C10 C C sing 1.51 N N
28 C10 C11 C C sing 1.53 N N
29 C11 C12 C C sing 1.53 N N
30 C12 C13 C C sing 1.53 N N
31 C13 C14 C C sing 1.53 N N
32 C14 C15 C C sing 1.53 N N
33 C15 C16 C C sing 1.53 N N
34 C16 C17 C C sing 1.53 N N
35 C17 C18 C C sing 1.53 N N
36 C18 O2 C O sing 1.43 N N
37 N1 H1 N H sing 0.97 N N
38 C7 H7 C H sing 1.09 N N
39 C1 HA C H sing 1.09 N N
40 C2 H21C C H sing 1.09 N N
41 C2 H22C C H sing 1.09 N N
42 C3 H31C C H sing 1.09 N N
43 C3 H32C C H sing 1.09 N N
44 C4 H41C C H sing 1.09 N N
45 C4 H42C C H sing 1.09 N N
46 C5 H51C C H sing 1.09 N N
47 C5 H52C C H sing 1.09 N N
48 N HN1 N H sing 1.01 N N
49 N HN2 N H sing 1.01 N N
50 N3 H3 N H sing 0.97 N N
51 C19 H191 C H sing 1.09 N N
52 C19 H192 C H sing 1.09 N N
53 C20 H201 C H sing 1.09 N N
54 C20 H202 C H sing 1.09 N N
55 C21 H21 C H sing 1.09 N N
56 C26 H261 C H sing 1.09 N N
57 C26 H262 C H sing 1.09 N N
58 C22 H221 C H sing 1.09 N N
59 C22 H222 C H sing 1.09 N N
60 C25 H251 C H sing 1.09 N N
61 C25 H252 C H sing 1.09 N N
62 C24 H241 C H sing 1.09 N N
63 C24 H242 C H sing 1.09 N N
64 C23 H231 C H sing 1.09 N N
65 C23 H232 C H sing 1.09 N N
66 C8 H81C C H sing 1.09 N N
67 C8 H82C C H sing 1.09 N N
68 N2 H2 N H sing 0.97 N N
69 O1 HB O H sing 0.97 N N
70 C10 H101 C H sing 1.09 N N
71 C10 H102 C H sing 1.09 N N
72 C11 H111 C H sing 1.09 N N
73 C11 H112 C H sing 1.09 N N
74 C12 H121 C H sing 1.09 N N
75 C12 H122 C H sing 1.09 N N
76 C13 H131 C H sing 1.09 N N
77 C13 H132 C H sing 1.09 N N
78 C14 H141 C H sing 1.09 N N
79 C14 H142 C H sing 1.09 N N
80 C15 H151 C H sing 1.09 N N
81 C15 H152 C H sing 1.09 N N
82 C16 H161 C H sing 1.09 N N
83 C16 H162 C H sing 1.09 N N
84 C17 H171 C H sing 1.09 N N
85 C17 H172 C H sing 1.09 N N
86 C18 H181 C H sing 1.09 N N
87 C18 H182 C H sing 1.09 N N
88 O2 HC O H sing 0.97 N N



JJ1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JJ1 4c7i Open in New Window Bound ligand 1 1