Chemical Components in the PDB

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7C7 : Summary

Code

7C7

One-letter code

X

Molecule name

N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide
OpenEye OEToolkits 1.7.6 (2S)-N',N'-diethyl-N-[(2S)-3-methoxy-1-(naphthalen-1-ylmethylamino)-1-oxidanylidene-propan-2-yl]-2-(3-phenylpropanoylamino)butanediamide

Formula

C32 H40 N4 O5

Formal charge

0

Molecular weight

560.684 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(NC(C(=O)NC(C(=O)NCc1c2c(ccc1)cccc2)COC)CC(N(CC)CC)=O)(=O)CCc3ccccc3
SMILES CACTVS 3.385 CCN(CC)C(=O)C[CH](NC(=O)CCc1ccccc1)C(=O)N[CH](COC)C(=O)NCc2cccc3ccccc23
SMILES OpenEye OEToolkits 1.7.6 CCN(CC)C(=O)CC(C(=O)NC(COC)C(=O)NCc1cccc2c1cccc2)NC(=O)CCc3ccccc3
Canonical SMILES CACTVS 3.385 CCN(CC)C(=O)C[C@H](NC(=O)CCc1ccccc1)C(=O)N[C@@H](COC)C(=O)NCc2cccc3ccccc23
Canonical SMILES OpenEye OEToolkits 1.7.6 CCN(CC)C(=O)C[C@@H](C(=O)N[C@@H](COC)C(=O)NCc1cccc2c1cccc2)NC(=O)CCc3ccccc3

IUPAC InChI

InChI=1S/C32H40N4O5/c1-4-36(5-2)30(38)20-27(34-29(37)19-18-23-12-7-6-8-13-23)32(40)35-28(22-41-3)31(39)33-21-25-16-11-15-24-14-9-10-17-26(24)25/h6-17,27-28H,4-5,18-22H2,1-3H3,(H,33,39)(H,34,37)(H,35,40)/t27-,28-/m0/s1

IUPAC InChI key

VBXXQNRGFBZKES-NSOVKSMOSA-N
7C7

wwPDB Information

Atom count

81 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-10-03

Last modified at

2017-01-06

Status

Released

Obsoleted

Not Assigned



7C7 : Atoms of Molecule

Total Number of Atoms: 81
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C32 C C24 N N N 0 3.807 -0.643 0.34
2 O41 O O5 N N N 0 3.356 -1.07 1.382
3 C33 C C25 N N N 0 4.997 -1.314 -0.297
4 C34 C C26 N N N 0 5.442 -2.494 0.57
5 C35 C C27 N Y N 0 6.631 -3.164 -0.067
6 C36 C C28 N Y N 0 7.911 -2.748 0.249
7 C37 C C29 N Y N 0 9.002 -3.363 -0.336
8 C38 C C30 N Y N 0 8.814 -4.394 -1.237
9 C39 C C31 N Y N 0 7.534 -4.811 -1.553
10 C40 C C32 N Y N 0 6.443 -4.2 -0.964
11 O01 O O2 N N N 0 0.982 -0.745 -0.883
12 C02 C C7 N N N 0 0.825 0.215 -0.158
13 C22 C C17 S N N 0 2.018 1.01 0.307
14 C23 C C18 N N N 0 1.881 2.458 -0.167
15 C24 C C19 N N N 0 3.0 3.285 0.412
16 N25 N N3 N N N 0 3.145 4.574 0.046
17 C26 C C20 N N N 0 4.234 5.377 0.609
18 C27 C C21 N N N 0 5.473 5.251 -0.28
19 C28 C C22 N N N 0 2.216 5.171 -0.916
20 C29 C C23 N N N 0 1.031 5.785 -0.166
21 O30 O O4 N N N 0 3.77 2.79 1.208
22 N31 N N4 N N N 0 3.241 0.428 -0.251
23 O20 O O1 N N N 0 -2.125 -0.936 2.017
24 N03 N N1 N N N 0 -0.415 0.569 0.232
25 C04 C C8 S N N 0 -1.574 -0.204 -0.219
26 C05 C C9 N N N 0 -2.802 0.67 -0.196
27 O18 O O3 N N N 0 -2.717 1.825 0.164
28 C19 C C15 N N N 0 -1.783 -1.401 0.71
29 C21 C C16 N N N 0 -2.342 -1.98 2.968
30 C11 C C1 N Y N 0 -8.588 -1.237 -1.913
31 C10 C C2 N Y N 0 -7.935 -0.375 -2.739
32 C12 C C3 N Y N 0 -8.152 -1.395 -0.586
33 C14 C C4 N Y N 0 -6.595 -0.812 1.196
34 C13 C C5 N Y N 0 -7.032 -0.655 -0.131
35 C15 C C6 N Y N 0 -7.252 -1.67 2.023
36 N06 N N2 N N N 0 -3.994 0.168 -0.573
37 C07 C C10 N N N 0 -5.187 1.018 -0.55
38 C08 C C11 N Y N 0 -6.38 0.222 -1.015
39 C09 C C12 N Y N 0 -6.834 0.352 -2.291
40 C16 C C13 N Y N 0 -8.354 -2.397 1.576
41 C17 C C14 N Y N 0 -8.804 -2.271 0.298
42 H32 H H32 N N N 0 4.723 -1.674 -1.288
43 H33 H H33 N N N 0 5.814 -0.598 -0.384
44 H34 H H34 N N N 0 5.715 -2.133 1.561
45 H38 H H38 N N N 0 9.666 -4.874 -1.694
46 H35 H H35 N N N 0 4.624 -3.21 0.656
47 H36 H H36 N N N 0 8.058 -1.942 0.953
48 H37 H H37 N N N 0 10.002 -3.038 -0.089
49 H39 H H39 N N N 0 7.387 -5.616 -2.257
50 H40 H H40 N N N 0 5.443 -4.525 -1.211
51 H18 H H18 N N N 0 2.068 0.988 1.395
52 H19 H H19 N N N 0 1.931 2.491 -1.256
53 H20 H H20 N N N 0 0.923 2.86 0.164
54 H21 H H21 N N N 0 3.926 6.421 0.658
55 H22 H H22 N N N 0 4.468 5.019 1.612
56 H23 H H23 N N N 0 6.282 5.848 0.139
57 H24 H H24 N N N 0 5.78 4.206 -0.329
58 H25 H H25 N N N 0 5.239 5.608 -1.283
59 H26 H H26 N N N 0 2.728 5.948 -1.483
60 H27 H H27 N N N 0 1.854 4.402 -1.598
61 H28 H H28 N N N 0 0.518 5.008 0.401
62 H29 H H29 N N N 0 1.393 6.554 0.517
63 H30 H H30 N N N 0 0.34 6.23 -0.881
64 H31 H H31 N N N 0 3.643 0.812 -1.045
65 H5 H H5 N N N 0 -0.54 1.336 0.813
66 H6 H H6 N N N 0 -1.401 -0.559 -1.235
67 H13 H H13 N N N 0 -0.864 -1.985 0.762
68 H14 H H14 N N N 0 -2.589 -2.025 0.324
69 H15 H H15 N N N 0 -3.16 -2.616 2.629
70 H16 H H16 N N N 0 -1.435 -2.576 3.067
71 H17 H H17 N N N 0 -2.597 -1.544 3.934
72 H1 H H1 N N N 0 -9.44 -1.794 -2.273
73 H2 H H2 N N N 0 -8.274 -0.253 -3.757
74 H3 H H3 N N N 0 -5.743 -0.255 1.556
75 H4 H H4 N N N 0 -6.915 -1.789 3.042
76 H7 H H7 N N N 0 -4.062 -0.756 -0.86
77 H8 H H8 N N N 0 -5.361 1.372 0.466
78 H9 H H9 N N N 0 -5.039 1.87 -1.212
79 H10 H H10 N N N 0 -6.333 1.029 -2.968
80 H11 H H11 N N N 0 -8.857 -3.071 2.253
81 H12 H H12 N N N 0 -9.659 -2.841 -0.035



7C7 : Chemical Bonds

Total Number of Bonds: 83
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C39 C38 C C doub 1.38 N Y
2 C39 C40 C C sing 1.38 N Y
3 C38 C37 C C sing 1.38 N Y
4 C40 C35 C C doub 1.38 N Y
5 C37 C36 C C doub 1.38 N Y
6 C35 C36 C C sing 1.38 N Y
7 C35 C34 C C sing 1.51 N N
8 C34 C33 C C sing 1.53 N N
9 C33 C32 C C sing 1.51 N N
10 O41 C32 O C doub 1.21 N N
11 C32 N31 C N sing 1.35 N N
12 N31 C22 N C sing 1.46 N N
13 O30 C24 O C doub 1.21 N N
14 C22 C02 C C sing 1.51 N N
15 C22 C23 C C sing 1.53 N N
16 C27 C26 C C sing 1.53 N N
17 C19 O20 C O sing 1.43 N N
18 C19 C04 C C sing 1.53 N N
19 C24 C23 C C sing 1.51 N N
20 C24 N25 C N sing 1.35 N N
21 C02 N03 C N sing 1.35 N N
22 C02 O01 C O doub 1.21 N N
23 N03 C04 N C sing 1.46 N N
24 C26 N25 C N sing 1.47 N N
25 C21 O20 C O sing 1.43 N N
26 N25 C28 N C sing 1.46 N N
27 C04 C05 C C sing 1.51 N N
28 C28 C29 C C sing 1.53 N N
29 C05 O18 C O doub 1.21 N N
30 C05 N06 C N sing 1.35 N N
31 N06 C07 N C sing 1.47 N N
32 C07 C08 C C sing 1.51 N N
33 C14 C15 C C doub 1.36 N Y
34 C14 C13 C C sing 1.41 N Y
35 C15 C16 C C sing 1.39 N Y
36 C08 C13 C C doub 1.41 N Y
37 C08 C09 C C sing 1.36 N Y
38 C13 C12 C C sing 1.42 N Y
39 C16 C17 C C doub 1.36 N Y
40 C09 C10 C C doub 1.39 N Y
41 C12 C17 C C sing 1.4 N Y
42 C12 C11 C C doub 1.41 N Y
43 C10 C11 C C sing 1.36 N Y
44 C11 H1 C H sing 1.08 N N
45 C10 H2 C H sing 1.08 N N
46 C14 H3 C H sing 1.08 N N
47 C15 H4 C H sing 1.08 N N
48 N03 H5 N H sing 0.97 N N
49 C04 H6 C H sing 1.09 N N
50 N06 H7 N H sing 0.97 N N
51 C07 H8 C H sing 1.09 N N
52 C07 H9 C H sing 1.09 N N
53 C09 H10 C H sing 1.08 N N
54 C16 H11 C H sing 1.08 N N
55 C17 H12 C H sing 1.08 N N
56 C19 H13 C H sing 1.09 N N
57 C19 H14 C H sing 1.09 N N
58 C21 H15 C H sing 1.09 N N
59 C21 H16 C H sing 1.09 N N
60 C21 H17 C H sing 1.09 N N
61 C22 H18 C H sing 1.09 N N
62 C23 H19 C H sing 1.09 N N
63 C23 H20 C H sing 1.09 N N
64 C26 H21 C H sing 1.09 N N
65 C26 H22 C H sing 1.09 N N
66 C27 H23 C H sing 1.09 N N
67 C27 H24 C H sing 1.09 N N
68 C27 H25 C H sing 1.09 N N
69 C28 H26 C H sing 1.09 N N
70 C28 H27 C H sing 1.09 N N
71 C29 H28 C H sing 1.09 N N
72 C29 H29 C H sing 1.09 N N
73 C29 H30 C H sing 1.09 N N
74 N31 H31 N H sing 0.97 N N
75 C33 H32 C H sing 1.09 N N
76 C33 H33 C H sing 1.09 N N
77 C34 H34 C H sing 1.09 N N
78 C34 H35 C H sing 1.09 N N
79 C36 H36 C H sing 1.08 N N
80 C37 H37 C H sing 1.08 N N
81 C38 H38 C H sing 1.08 N N
82 C39 H39 C H sing 1.08 N N
83 C40 H40 C H sing 1.08 N N



7C7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
7C7 5tho Open in New Window Bound ligand 14 1