Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

6KG : Summary

Code

6KG

One-letter code

X

Molecule name

Nalpha-[(2S)-2-{[(2S)-2-azido-3-phenylpropanoyl]amino}-4-cyclohexylbutanoyl]-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide

Systematic names

ProgramVersionName
ACDLabs 12.01 Nalpha-[(2S)-2-{[(2S)-2-azido-3-phenylpropanoyl]amino}-4-cyclohexylbutanoyl]-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide
OpenEye OEToolkits 2.0.4 (2~{S})-2-[[(2~{S})-2-azido-3-phenyl-propanoyl]amino]-4-cyclohexyl-~{N}-[(2~{S})-1-[[(2~{R},3~{S},4~{S})-2,6-dimethyl-1,3-bis(oxidanyl)heptan-4-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]butanamide

Formula

C37 H54 N6 O5

Formal charge

0

Molecular weight

662.862 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1ccc(cc1)CC(C(NC(C(=O)NC(Cc2ccccc2)C(NC(CC(C)C)C(O)C(C)CO)=O)CCC3CCCCC3)=O)N=[N+]=[N-]
SMILES CACTVS 3.385 CC(C)C[CH](NC(=O)[CH](Cc1ccccc1)NC(=O)[CH](CCC2CCCCC2)NC(=O)[CH](Cc3ccccc3)N=[N+]=[N-])[CH](O)[CH](C)CO
SMILES OpenEye OEToolkits 2.0.4 CC(C)CC(C(C(C)CO)O)NC(=O)C(Cc1ccccc1)NC(=O)C(CCC2CCCCC2)NC(=O)C(Cc3ccccc3)N=[N+]=[N-]
Canonical SMILES CACTVS 3.385 CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCC2CCCCC2)NC(=O)[C@H](Cc3ccccc3)N=[N+]=[N-])[C@@H](O)[C@H](C)CO
Canonical SMILES OpenEye OEToolkits 2.0.4 C[C@H](CO)[C@@H]([C@H](CC(C)C)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCC2CCCCC2)NC(=O)[C@H](Cc3ccccc3)N=[N+]=[N-])O

IUPAC InChI

InChI=1S/C37H54N6O5/c1-25(2)21-31(34(45)26(3)24-44)40-36(47)32(22-28-15-9-5-10-16-28)41-35(46)30(20-19-27-13-7-4-8-14-27)39-37(48)33(42-43-38)23-29-17-11-6-12-18-29/h5-6,9-12,15-18,25-27,30-34,44-45H,4,7-8,13-14,19-24H2,1-3H3,(H,39,48)(H,40,47)(H,41,46)/t26-,30+,31+,32+,33+,34+/m1/s1

IUPAC InChI key

OENPGYKZUFVMPA-DZPCQTFRSA-N
6KG

wwPDB Information

Atom count

102 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-04-22

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



6KG : Atoms of Molecule

Total Number of Atoms: 102
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 8.586 3.014 1.627
2 C5 C C2 N Y N 0 8.641 2.584 0.314
3 C6 C C3 N Y N 0 7.492 2.144 -0.317
4 C7 C C4 N N N 0 5.038 1.653 -0.324
5 C8 C C5 S N N 0 4.882 0.147 -0.107
6 C15 C C6 S N N 0 1.15 -0.573 -0.567
7 C17 C C7 N N N 0 2.006 -2.89 -0.945
8 C20 C C8 N N N 0 2.569 -6.696 -1.094
9 C21 C C9 N N N 0 2.795 -6.926 0.402
10 C22 C C10 N N N 0 1.804 -6.079 1.203
11 C24 C C11 N N N 0 0.027 0.239 0.025
12 C28 C C12 N N N 0 -2.499 2.092 -0.568
13 C2 C C13 N Y N 0 6.234 2.569 1.675
14 C3 C C14 N Y N 0 7.383 3.004 2.308
15 C1 C C15 N Y N 0 6.29 2.133 0.364
16 N9 N N1 N N N 0 5.983 -0.559 -0.768
17 N10 N N2 N N N 1 7.038 -0.413 -0.411
18 N11 N N3 N N N -1 8.094 -0.268 -0.054
19 C12 C C16 N N N 0 3.57 -0.312 -0.689
20 O13 O O1 N N N 0 3.543 -0.846 -1.778
21 N14 N N4 N N N 0 2.426 -0.128 -0.001
22 C16 C C17 N N N 0 0.937 -2.053 -0.241
23 C18 C C18 N N N 0 1.793 -4.37 -0.619
24 C19 C C19 N N N 0 2.783 -5.217 -1.42
25 C23 C C20 N N N 0 2.018 -4.6 0.877
26 O25 O O2 N N N 0 0.268 1.104 0.839
27 N26 N N5 N N N 0 -1.245 0.003 -0.351
28 C27 C C21 S N N 0 -2.337 0.793 0.224
29 C29 C C22 N Y N 0 -1.264 2.939 -0.4
30 C30 C C23 N Y N 0 -1.184 3.847 0.639
31 C31 C C24 N Y N 0 -0.051 4.624 0.792
32 C32 C C25 N Y N 0 1.002 4.493 -0.094
33 C33 C C26 N Y N 0 0.923 3.584 -1.133
34 C34 C C27 N Y N 0 -0.208 2.804 -1.283
35 C35 C C28 N N N 0 -3.618 0.001 0.158
36 O36 O O3 N N N 0 -3.619 -1.112 -0.322
37 N37 N N6 N N N 0 -4.763 0.531 0.632
38 C38 C C29 S N N 0 -6.027 -0.191 0.47
39 C40 C C31 N N N 0 -7.474 -1.993 1.419
40 C39 C C30 N N N 0 -6.23 -1.135 1.657
41 C42 C C32 N N N 0 -7.237 -2.914 0.221
42 C41 C C33 N N N 0 -7.757 -2.838 2.663
43 C43 C C34 S N N 0 -7.183 0.81 0.411
44 O44 O O4 N N N 0 -7.284 1.495 1.661
45 C45 C C35 R N N 0 -6.924 1.822 -0.706
46 C48 C C36 N N N 0 -8.004 2.905 -0.673
47 C46 C C37 N N N 0 -6.959 1.108 -2.059
48 O47 O O5 N N N 0 -6.603 2.029 -3.092
49 H1 H H1 N N N 0 9.484 3.355 2.122
50 H2 H H2 N N N 0 9.58 2.593 -0.218
51 H3 H H3 N N N 0 7.535 1.808 -1.343
52 H4 H H4 N N N 0 5.108 1.86 -1.392
53 H5 H H5 N N N 0 4.174 2.171 0.091
54 H6 H H6 N N N 0 4.901 -0.07 0.961
55 H7 H H7 N N N 0 1.166 -0.438 -1.648
56 H8 H H8 N N N 0 1.933 -2.741 -2.022
57 H9 H H9 N N N 0 2.994 -2.581 -0.601
58 H10 H H10 N N N 0 3.275 -7.3 -1.665
59 H11 H H11 N N N 0 1.551 -6.983 -1.356
60 H12 H H12 N N N 0 2.642 -7.981 0.634
61 H13 H H13 N N N 0 3.813 -6.64 0.664
62 H14 H H14 N N N 0 0.786 -6.366 0.941
63 H15 H H15 N N N 0 1.965 -6.243 2.269
64 H16 H H16 N N N 0 -2.64 1.859 -1.623
65 H17 H H17 N N N 0 -3.367 2.638 -0.197
66 H18 H H18 N N N 0 5.294 2.56 2.207
67 H19 H H19 N N N 0 7.341 3.335 3.335
68 H21 H H21 N N N 0 2.447 0.299 0.87
69 H22 H H22 N N N 0 1.01 -2.202 0.837
70 H23 H H23 N N N 0 -0.051 -2.362 -0.584
71 H24 H H24 N N N 0 0.774 -4.656 -0.881
72 H25 H H25 N N N 0 3.802 -4.93 -1.158
73 H26 H H26 N N N 0 2.623 -5.053 -2.485
74 H27 H H27 N N N 0 1.312 -3.996 1.448
75 H28 H H28 N N N 0 3.036 -4.313 1.14
76 H29 H H29 N N N 0 -1.439 -0.689 -1.003
77 H30 H H30 N N N 0 -2.108 1.026 1.264
78 H31 H H31 N N N 0 -2.006 3.949 1.331
79 H32 H H32 N N N 0 0.012 5.334 1.603
80 H33 H H33 N N N 0 1.887 5.101 0.025
81 H34 H H34 N N N 0 1.745 3.482 -1.825
82 H35 H H35 N N N 0 -0.269 2.091 -2.092
83 H36 H H36 N N N 0 -4.75 1.391 1.081
84 H37 H H37 N N N 0 -5.999 -0.769 -0.453
85 H38 H H38 N N N 0 -5.358 -1.781 1.761
86 H39 H H39 N N N 0 -6.361 -0.551 2.568
87 H40 H H40 N N N 0 -8.328 -1.347 1.217
88 H41 H H41 N N N 0 -8.149 -3.471 0.004
89 H42 H H42 N N N 0 -6.962 -2.316 -0.648
90 H43 H H43 N N N 0 -6.432 -3.611 0.452
91 H44 H H44 N N N 0 -6.903 -3.485 2.865
92 H45 H H45 N N N 0 -7.926 -2.182 3.517
93 H46 H H46 N N N 0 -8.644 -3.449 2.493
94 H47 H H47 N N N 0 -8.113 0.278 0.212
95 H48 H H48 N N N 0 -6.489 1.99 1.903
96 H49 H H49 N N N 0 -5.945 2.28 -0.562
97 H50 H H50 N N N 0 -8.988 2.44 -0.728
98 H51 H H51 N N N 0 -7.922 3.472 0.254
99 H52 H H52 N N N 0 -7.872 3.576 -1.522
100 H53 H H53 N N N 0 -6.251 0.28 -2.051
101 H55 H H55 N N N 0 -6.604 1.644 -3.98
102 H54 H H54 N N N 0 -7.963 0.727 -2.243



6KG : Chemical Bonds

Total Number of Bonds: 104
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 C4 C C doub 1.38 N Y
2 C5 C6 C C sing 1.38 N Y
3 C4 C3 C C sing 1.38 N Y
4 C6 C1 C C doub 1.38 N Y
5 C3 C2 C C doub 1.38 N Y
6 C1 C2 C C sing 1.38 N Y
7 C1 C7 C C sing 1.51 N N
8 C7 C8 C C sing 1.53 N N
9 C22 C21 C C sing 1.53 N N
10 C22 C23 C C sing 1.53 N N
11 C21 C20 C C sing 1.53 N N
12 O13 C12 O C doub 1.21 N N
13 C23 C18 C C sing 1.53 N N
14 C8 C12 C C sing 1.51 N N
15 C8 N9 C N sing 1.47 N N
16 C12 N14 C N sing 1.35 N N
17 N11 N10 N N doub 1.12 N N
18 N10 N9 N N doub 1.12 N N
19 C20 C19 C C sing 1.53 N N
20 C18 C19 C C sing 1.53 N N
21 C18 C17 C C sing 1.53 N N
22 C16 C17 C C sing 1.53 N N
23 C16 C15 C C sing 1.53 N N
24 N14 C15 N C sing 1.47 N N
25 C15 C24 C C sing 1.51 N N
26 C24 O25 C O doub 1.21 N N
27 C24 N26 C N sing 1.35 N N
28 C31 C30 C C doub 1.38 N Y
29 C31 C32 C C sing 1.38 N Y
30 N26 C27 N C sing 1.47 N N
31 C30 C29 C C sing 1.38 N Y
32 C32 C33 C C doub 1.38 N Y
33 C27 C28 C C sing 1.53 N N
34 C27 C35 C C sing 1.51 N N
35 C29 C28 C C sing 1.51 N N
36 C29 C34 C C doub 1.38 N Y
37 O36 C35 O C doub 1.21 N N
38 C33 C34 C C sing 1.38 N Y
39 C35 N37 C N sing 1.35 N N
40 N37 C38 N C sing 1.46 N N
41 C41 C40 C C sing 1.53 N N
42 O47 C46 O C sing 1.43 N N
43 C48 C45 C C sing 1.53 N N
44 C40 C42 C C sing 1.53 N N
45 C40 C39 C C sing 1.53 N N
46 C38 C39 C C sing 1.53 N N
47 C38 C43 C C sing 1.53 N N
48 C46 C45 C C sing 1.53 N N
49 C45 C43 C C sing 1.53 N N
50 C43 O44 C O sing 1.43 N N
51 C4 H1 C H sing 1.08 N N
52 C5 H2 C H sing 1.08 N N
53 C6 H3 C H sing 1.08 N N
54 C7 H4 C H sing 1.09 N N
55 C7 H5 C H sing 1.09 N N
56 C8 H6 C H sing 1.09 N N
57 C15 H7 C H sing 1.09 N N
58 C17 H8 C H sing 1.09 N N
59 C17 H9 C H sing 1.09 N N
60 C20 H10 C H sing 1.09 N N
61 C20 H11 C H sing 1.09 N N
62 C21 H12 C H sing 1.09 N N
63 C21 H13 C H sing 1.09 N N
64 C22 H14 C H sing 1.09 N N
65 C22 H15 C H sing 1.09 N N
66 C28 H16 C H sing 1.09 N N
67 C28 H17 C H sing 1.09 N N
68 C2 H18 C H sing 1.08 N N
69 C3 H19 C H sing 1.08 N N
70 N14 H21 N H sing 0.97 N N
71 C16 H22 C H sing 1.09 N N
72 C16 H23 C H sing 1.09 N N
73 C18 H24 C H sing 1.09 N N
74 C19 H25 C H sing 1.09 N N
75 C19 H26 C H sing 1.09 N N
76 C23 H27 C H sing 1.09 N N
77 C23 H28 C H sing 1.09 N N
78 N26 H29 N H sing 0.97 N N
79 C27 H30 C H sing 1.09 N N
80 C30 H31 C H sing 1.08 N N
81 C31 H32 C H sing 1.08 N N
82 C32 H33 C H sing 1.08 N N
83 C33 H34 C H sing 1.08 N N
84 C34 H35 C H sing 1.08 N N
85 N37 H36 N H sing 0.97 N N
86 C38 H37 C H sing 1.09 N N
87 C39 H38 C H sing 1.09 N N
88 C39 H39 C H sing 1.09 N N
89 C40 H40 C H sing 1.09 N N
90 C42 H41 C H sing 1.09 N N
91 C42 H42 C H sing 1.09 N N
92 C42 H43 C H sing 1.09 N N
93 C41 H44 C H sing 1.09 N N
94 C41 H45 C H sing 1.09 N N
95 C41 H46 C H sing 1.09 N N
96 C43 H47 C H sing 1.09 N N
97 O44 H48 O H sing 0.97 N N
98 C45 H49 C H sing 1.09 N N
99 C48 H50 C H sing 1.09 N N
100 C48 H51 C H sing 1.09 N N
101 C48 H52 C H sing 1.09 N N
102 C46 H53 C H sing 1.09 N N
103 C46 H54 C H sing 1.09 N N
104 O47 H55 O H sing 0.97 N N



6KG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6KG 5jhs Open in New Window Bound ligand 3 1