Chemical Components in the PDB

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MM9 : Summary

Code

MM9

One-letter code

X

Molecule name

(2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(dimethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-N-(4-carbamimidoylbenzyl)-1-[(2R)-2-cyclohexyl-2-{[2-(dimethylamino)-2-oxoethyl]amino}acetyl]azetidine-2-carboxamide
OpenEye OEToolkits 1.9.2 (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(dimethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide

Formula

C24 H36 N6 O3

Formal charge

0

Molecular weight

456.581 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCc1ccc(C(=[N@H])N)cc1)C3N(C(=O)C(NCC(=O)N(C)C)C2CCCCC2)CC3
SMILES CACTVS 3.385 CN(C)C(=O)CN[CH](C1CCCCC1)C(=O)N2CC[CH]2C(=O)NCc3ccc(cc3)C(N)=N
SMILES OpenEye OEToolkits 1.9.2 CN(C)C(=O)CNC(C1CCCCC1)C(=O)N2CCC2C(=O)NCc3ccc(cc3)C(=N)N
Canonical SMILES CACTVS 3.385 CN(C)C(=O)CN[C@H](C1CCCCC1)C(=O)N2CC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
Canonical SMILES OpenEye OEToolkits 1.9.2 [H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCN2C(=O)[C@@H](C3CCCCC3)NCC(=O)N(C)C)\N

IUPAC InChI

InChI=1S/C24H36N6O3/c1-29(2)20(31)15-27-21(17-6-4-3-5-7-17)24(33)30-13-12-19(30)23(32)28-14-16-8-10-18(11-9-16)22(25)26/h8-11,17,19,21,27H,3-7,12-15H2,1-2H3,(H3,25,26)(H,28,32)/t19-,21+/m0/s1

IUPAC InChI key

UBUHFANKPRTXGI-PZJWPPBQSA-N
MM9

wwPDB Information

Atom count

69 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-09-14

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



MM9 : Atoms of Molecule

Total Number of Atoms: 69
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -3.766 1.729 0.007
2 C2 C C2 N N N 0 -3.119 2.819 0.865
3 C3 C C3 N N N 0 -3.669 4.186 0.452
4 C4 C C4 N N N 0 -3.348 4.44 -1.022
5 C5 C C5 N N N 0 -3.994 3.351 -1.88
6 C6 C C6 N N N 0 -3.445 1.984 -1.468
7 N7 N N7 N N N 0 -3.934 -0.694 -0.307
8 C8 C C8 R N N 0 -3.216 0.362 0.419
9 C9 C C9 N N N 0 -1.748 0.29 0.088
10 O0 O O0 N N N 0 -1.386 -0.192 -0.964
11 N11 N N11 N N N 0 -0.836 0.761 0.962
12 C12 C C12 S N N 0 0.624 0.935 0.978
13 C13 C C13 N N N 0 1.37 -0.191 0.31
14 O14 O O14 N N N 0 0.759 -1.12 -0.174
15 N15 N N15 N N N 0 2.716 -0.166 0.25
16 C16 C C16 N N N 0 3.441 -1.26 -0.4
17 C17 C C17 N Y N 0 4.922 -0.992 -0.333
18 C18 C C18 N Y N 0 5.657 -1.452 0.745
19 C19 C C19 N Y N 0 7.014 -1.209 0.813
20 C20 C C20 N Y N 0 7.644 -0.498 -0.208
21 C21 C C21 N Y N 0 6.898 -0.037 -1.292
22 C22 C C22 N Y N 0 5.543 -0.291 -1.351
23 C23 C C23 N N N 0 9.099 -0.233 -0.141
24 N24 N N24 N N N 0 9.794 -0.665 0.873
25 N25 N N25 N N N 0 9.719 0.47 -1.151
26 C26 C C26 N N N 0 0.568 0.808 2.507
27 C27 C C27 N N N 0 -0.864 1.333 2.317
28 C28 C C28 N N N 0 -5.221 -0.993 0.335
29 C10 C C10 N N N 0 -7.694 -3.759 -0.609
30 C29 C C29 N N N 0 -5.868 -2.165 -0.357
31 O30 O O30 N N N 0 -5.312 -2.698 -1.293
32 C30 C C30 N N N 0 -7.737 -1.975 1.195
33 N2 N N2 N N N 0 -7.065 -2.62 0.064
34 H22 H H22 N N N 0 0.948 1.917 0.635
35 H1 H H1 N N N 0 -4.846 1.745 0.152
36 H21C H H21C N N N 0 -3.348 2.637 1.915
37 H22C H H22C N N N 0 -2.039 2.802 0.72
38 H61C H H61C N N N 0 -2.365 1.967 -1.612
39 H62C H H62C N N N 0 -3.905 1.207 -2.079
40 H8 H H8 N N N 0 -3.354 0.224 1.492
41 H31C H H31C N N N 0 -4.749 4.202 0.597
42 H32C H H32C N N N 0 -3.208 4.962 1.063
43 H41C H H41C N N N 0 -3.74 5.414 -1.316
44 H42C H H42C N N N 0 -2.268 4.424 -1.167
45 H51C H H51C N N N 0 -5.075 3.367 -1.735
46 H52C H H52C N N N 0 -3.766 3.532 -2.931
47 H7 H H7 N N N 0 -4.063 -0.443 -1.276
48 H281 H H281 N N N 0 -5.056 -1.237 1.385
49 H282 H H282 N N N 0 -5.874 -0.123 0.264
50 H271 H H271 N N N 0 -0.933 2.421 2.327
51 H272 H H272 N N N 0 -1.593 0.858 2.973
52 H261 H H261 N N N 0 0.627 -0.217 2.873
53 H262 H H262 N N N 0 1.227 1.496 3.037
54 H15 H H15 N N N 0 3.205 0.577 0.637
55 H161 H H161 N N N 0 3.218 -2.197 0.11
56 H162 H H162 N N N 0 3.132 -1.332 -1.443
57 H18 H H18 N N N 0 5.168 -2.003 1.535
58 HA H HA N N N 0 4.964 0.062 -2.192
59 H19 H H19 N N N 0 7.587 -1.568 1.655
60 H21 H H21 N N N 0 7.38 0.515 -2.086
61 H24 H H24 N N N 0 10.747 -0.491 0.917
62 H251 H H251 N N N 0 9.202 0.791 -1.906
63 H252 H H252 N N N 0 10.672 0.643 -1.107
64 H101 H H101 N N N 0 -7.377 -4.685 -0.129
65 H102 H H102 N N N 0 -8.778 -3.667 -0.543
66 H103 H H103 N N N 0 -7.394 -3.772 -1.657
67 H301 H H301 N N N 0 -8.685 -2.477 1.388
68 H302 H H302 N N N 0 -7.103 -2.042 2.08
69 H303 H H303 N N N 0 -7.922 -0.927 0.959



MM9 : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 C6 C C sing 1.53 N N
3 C1 C8 C C sing 1.53 N N
4 C2 C3 C C sing 1.53 N N
5 C3 C4 C C sing 1.53 N N
6 C4 C5 C C sing 1.53 N N
7 C5 C6 C C sing 1.53 N N
8 N7 C8 N C sing 1.47 N N
9 N7 C28 N C sing 1.47 N N
10 C8 C9 C C sing 1.51 N N
11 C9 O0 C O doub 1.21 N N
12 C9 N11 C N sing 1.35 N N
13 N11 C12 N C sing 1.47 N N
14 N11 C27 N C sing 1.47 N N
15 C12 C13 C C sing 1.51 N N
16 C12 C26 C C sing 1.54 N N
17 C13 O14 C O doub 1.21 N N
18 C13 N15 C N sing 1.35 N N
19 N15 C16 N C sing 1.46 N N
20 C16 C17 C C sing 1.51 N N
21 C17 C18 C C sing 1.38 N Y
22 C17 C22 C C doub 1.38 N Y
23 C18 C19 C C doub 1.38 N Y
24 C19 C20 C C sing 1.39 N Y
25 C20 C21 C C doub 1.39 N Y
26 C20 C23 C C sing 1.48 N N
27 C21 C22 C C sing 1.38 N Y
28 C23 N24 C N doub 1.3 N N
29 C23 N25 C N sing 1.38 N N
30 C26 C27 C C sing 1.54 N N
31 C28 C29 C C sing 1.51 N N
32 C10 N2 C N sing 1.46 N N
33 C29 O30 C O doub 1.21 N N
34 C29 N2 C N sing 1.35 N N
35 C30 N2 C N sing 1.47 N N
36 C12 H22 C H sing 1.09 N N
37 C1 H1 C H sing 1.09 N N
38 C2 H21C C H sing 1.09 N N
39 C2 H22C C H sing 1.09 N N
40 C6 H61C C H sing 1.09 N N
41 C6 H62C C H sing 1.09 N N
42 C8 H8 C H sing 1.09 N N
43 C3 H31C C H sing 1.09 N N
44 C3 H32C C H sing 1.09 N N
45 C4 H41C C H sing 1.09 N N
46 C4 H42C C H sing 1.09 N N
47 C5 H51C C H sing 1.09 N N
48 C5 H52C C H sing 1.09 N N
49 N7 H7 N H sing 1.01 N N
50 C28 H281 C H sing 1.09 N N
51 C28 H282 C H sing 1.09 N N
52 C27 H271 C H sing 1.09 N N
53 C27 H272 C H sing 1.09 N N
54 C26 H261 C H sing 1.09 N N
55 C26 H262 C H sing 1.09 N N
56 N15 H15 N H sing 0.97 N N
57 C16 H161 C H sing 1.09 N N
58 C16 H162 C H sing 1.09 N N
59 C18 H18 C H sing 1.08 N N
60 C22 HA C H sing 1.08 N N
61 C19 H19 C H sing 1.08 N N
62 C21 H21 C H sing 1.08 N N
63 N24 H24 N H sing 0.97 N N
64 N25 H251 N H sing 0.97 N N
65 N25 H252 N H sing 0.97 N N
66 C10 H101 C H sing 1.09 N N
67 C10 H102 C H sing 1.09 N N
68 C10 H103 C H sing 1.09 N N
69 C30 H301 C H sing 1.09 N N
70 C30 H302 C H sing 1.09 N N
71 C30 H303 C H sing 1.09 N N



MM9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
MM9 4bam Open in New Window Bound ligand 1 1