Chemical Components in the PDB

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A1L : Summary

Code

A1L

One-letter code

X

Molecule name

[2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-diazonio-azanide

Systematic names

ProgramVersionName
ACDLabs 12.01 N~2~-(azidoacetyl)-N,N-dibenzyl-N~5~-[N-(methylcarbamoyl)carbamimidoyl]-L-ornithinamide
OpenEye OEToolkits 1.7.6 [2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-diazonio-azanide

Formula

C24 H31 N9 O3

Formal charge

0

Molecular weight

493.561 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N#[N+][N-]CC(=O)NC(C(=O)N(Cc1ccccc1)Cc2ccccc2)CCCNC(=[N@H])NC(=O)NC
SMILES CACTVS 3.385 CNC(=O)NC(=N)NCCC[CH](NC(=O)C[N-][N+]#N)C(=O)N(Cc1ccccc1)Cc2ccccc2
SMILES OpenEye OEToolkits 1.7.6 CNC(=O)NC(=N)NCCCC(C(=O)N(Cc1ccccc1)Cc2ccccc2)NC(=O)C[N-][N+]#N
Canonical SMILES CACTVS 3.385 CNC(=O)NC(=N)NCCC[C@H](NC(=O)C[N-][N+]#N)C(=O)N(Cc1ccccc1)Cc2ccccc2
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C(\NCCC[C@@H](C(=O)N(Cc1ccccc1)Cc2ccccc2)NC(=O)C[N-][N+]#N)/NC(=O)NC

IUPAC InChI

InChI=1S/C24H31N9O3/c1-27-24(36)31-23(25)28-14-8-13-20(30-21(34)15-29-32-26)22(35)33(16-18-9-4-2-5-10-18)17-19-11-6-3-7-12-19/h2-7,9-12,20H,8,13-17H2,1H3,(H,30,34)(H4,25,27,28,31,36)/t20-/m0/s1

IUPAC InChI key

WCLXSHAWFUUDKF-FQEVSTJZSA-N
A1L

wwPDB Information

Atom count

67 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-06-25

Last modified at

2013-09-13

Status

Released

Obsoleted

Not Assigned



A1L : Atoms of Molecule

Total Number of Atoms: 67
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C9 C C9 N N N 0 9.951 0.432 0.775
2 N6 N N6 N N N 0 8.615 0.142 1.302
3 C8 C C8 N N N 0 7.538 0.239 0.498
4 O3 O O3 N N N 0 7.675 0.567 -0.664
5 N4 N N4 N N N 0 6.309 -0.027 0.983
6 C7 C C7 N N N 0 5.206 0.072 0.159
7 N5 N N5 N N N 0 5.352 0.423 -1.086
8 N3 N N3 N N N 0 3.952 -0.2 0.653
9 C6 C C6 N N N 0 2.781 -0.094 -0.221
10 C5 C C5 N N N 0 1.52 -0.447 0.571
11 C4 C C4 N N N 0 0.287 -0.218 -0.306
12 C2 C C2 S N N 0 -0.978 -0.451 0.523
13 N2 N N2 N N N 0 -1.054 -1.862 0.91
14 C3 C C3 N N N 0 -1.104 -2.819 -0.038
15 O1 O O1 N N N 0 -1.086 -2.513 -1.211
16 C10 C C10 N N N 0 -1.183 -4.27 0.361
17 N7 N N7 N N N -1 -1.226 -5.105 -0.842
18 N8 N N8 N N N 1 -1.294 -6.349 -0.738
19 N9 N N9 N N N 0 -1.349 -7.378 -0.651
20 C1 C C1 N N N 0 -2.189 -0.089 -0.297
21 O2 O O2 N N N 0 -2.627 -0.874 -1.111
22 N1 N N1 N N N 0 -2.785 1.108 -0.126
23 C12 C C12 N N N 0 -2.197 2.096 0.781
24 C13 C C13 N Y N 0 -1.344 3.056 -0.006
25 C20 C C20 N Y N 0 -1.926 4.139 -0.64
26 C21 C C21 N Y N 0 -1.143 5.019 -1.363
27 C22 C C22 N Y N 0 0.222 4.817 -1.453
28 C23 C C23 N Y N 0 0.804 3.735 -0.82
29 C24 C C24 N Y N 0 0.022 2.858 -0.091
30 C11 C C11 N N N 0 -4.022 1.42 -0.847
31 C14 C C14 N Y N 0 -5.207 1.108 0.029
32 C15 C C15 N Y N 0 -5.712 -0.178 0.078
33 C16 C C16 N Y N 0 -6.796 -0.465 0.886
34 C17 C C17 N Y N 0 -7.375 0.533 1.646
35 C18 C C18 N Y N 0 -6.87 1.819 1.598
36 C19 C C19 N Y N 0 -5.786 2.107 0.79
37 H1 H H1 N N N 0 9.984 1.459 0.414
38 H2 H H2 N N N 0 10.69 0.301 1.566
39 H3 H H3 N N N 0 10.174 -0.25 -0.046
40 H4 H H4 N N N 0 8.506 -0.119 2.23
41 H5 H H5 N N N 0 6.2 -0.289 1.911
42 H6 H H6 N N N 0 4.577 0.493 -1.665
43 H7 H H7 N N N 0 3.843 -0.461 1.581
44 H8 H H8 N N N 0 2.7 0.925 -0.599
45 H9 H H9 N N N 0 2.89 -0.784 -1.058
46 H10 H H10 N N N 0 1.562 -1.493 0.873
47 H11 H H11 N N N 0 1.459 0.186 1.456
48 H12 H H12 N N N 0 0.293 0.806 -0.68
49 H13 H H13 N N N 0 0.305 -0.912 -1.146
50 H14 H H14 N N N 0 -0.945 0.17 1.418
51 H15 H H15 N N N 0 -1.069 -2.107 1.848
52 H16 H H16 N N N 0 -0.307 -4.533 0.954
53 H17 H H17 N N N 0 -2.085 -4.437 0.951
54 H19 H H19 N N N 0 -2.992 2.646 1.285
55 H20 H H20 N N N 0 -1.581 1.587 1.523
56 H21 H H21 N N N 0 -2.992 4.296 -0.57
57 H22 H H22 N N N 0 -1.598 5.864 -1.858
58 H23 H H23 N N N 0 0.833 5.505 -2.018
59 H24 H H24 N N N 0 1.87 3.578 -0.89
60 H25 H H25 N N N 0 0.477 2.013 0.404
61 H26 H H26 N N N 0 -4.032 2.478 -1.109
62 H27 H H27 N N N 0 -4.074 0.82 -1.756
63 H28 H H28 N N N 0 -5.259 -0.958 -0.516
64 H29 H H29 N N N 0 -7.19 -1.47 0.923
65 H30 H H30 N N N 0 -8.222 0.309 2.277
66 H31 H H31 N N N 0 -7.322 2.599 2.192
67 H32 H H32 N N N 0 -5.389 3.11 0.756



A1L : Chemical Bonds

Total Number of Bonds: 68
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N9 N8 N N trip 1.03 N N
2 N8 N7 N N sing 1.25 N N
3 N7 C10 N C sing 1.47 N N
4 C9 N6 C N sing 1.47 N N
5 C10 C3 C C sing 1.51 N N
6 O1 C3 O C doub 1.21 N N
7 O3 C8 O C doub 1.22 N N
8 C3 N2 C N sing 1.35 N N
9 N6 C8 N C sing 1.35 N N
10 C16 C17 C C doub 1.38 N Y
11 C16 C15 C C sing 1.38 N Y
12 C23 C22 C C doub 1.38 N Y
13 C23 C24 C C sing 1.38 N Y
14 C8 N4 C N sing 1.35 N N
15 C17 C18 C C sing 1.38 N Y
16 C22 C21 C C sing 1.38 N Y
17 C15 C14 C C doub 1.38 N Y
18 N2 C2 N C sing 1.47 N N
19 N5 C7 N C doub 1.3 N N
20 C24 C13 C C doub 1.38 N Y
21 N4 C7 N C sing 1.38 N N
22 C18 C19 C C doub 1.38 N Y
23 C7 N3 C N sing 1.37 N N
24 C21 C20 C C doub 1.38 N Y
25 C2 C1 C C sing 1.51 N N
26 C2 C4 C C sing 1.53 N N
27 C14 C19 C C sing 1.38 N Y
28 C14 C11 C C sing 1.51 N N
29 O2 C1 O C doub 1.21 N N
30 C13 C20 C C sing 1.38 N Y
31 C13 C12 C C sing 1.51 N N
32 C5 C4 C C sing 1.53 N N
33 C5 C6 C C sing 1.53 N N
34 C1 N1 C N sing 1.35 N N
35 N3 C6 N C sing 1.47 N N
36 N1 C11 N C sing 1.47 N N
37 N1 C12 N C sing 1.46 N N
38 C9 H1 C H sing 1.09 N N
39 C9 H2 C H sing 1.09 N N
40 C9 H3 C H sing 1.09 N N
41 N6 H4 N H sing 0.97 N N
42 N4 H5 N H sing 0.97 N N
43 N5 H6 N H sing 0.97 N N
44 N3 H7 N H sing 0.97 N N
45 C6 H8 C H sing 1.09 N N
46 C6 H9 C H sing 1.09 N N
47 C5 H10 C H sing 1.09 N N
48 C5 H11 C H sing 1.09 N N
49 C4 H12 C H sing 1.09 N N
50 C4 H13 C H sing 1.09 N N
51 C2 H14 C H sing 1.09 N N
52 N2 H15 N H sing 0.97 N N
53 C10 H16 C H sing 1.09 N N
54 C10 H17 C H sing 1.09 N N
55 C12 H19 C H sing 1.09 N N
56 C12 H20 C H sing 1.09 N N
57 C20 H21 C H sing 1.08 N N
58 C21 H22 C H sing 1.08 N N
59 C22 H23 C H sing 1.08 N N
60 C23 H24 C H sing 1.08 N N
61 C24 H25 C H sing 1.08 N N
62 C11 H26 C H sing 1.09 N N
63 C11 H27 C H sing 1.09 N N
64 C15 H28 C H sing 1.08 N N
65 C16 H29 C H sing 1.08 N N
66 C17 H30 C H sing 1.08 N N
67 C18 H31 C H sing 1.08 N N
68 C19 H32 C H sing 1.08 N N



A1L : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
A1L 3wd2 Open in New Window Bound ligand 1 1
A1L 3wd3 Open in New Window Bound ligand 1 1
A1L 3wd4 Open in New Window Bound ligand 1 1