Chemical Components in the PDB

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FD3 : Summary

Code

FD3

One-letter code

X

Molecule name

N-ALPHA-(2-NAPHTHYLSULFONYL)-3-AMIDINO-L-PHENYLALANINE PIPERAZIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-{(2S)-2-[(naphthalen-2-ylsulfonyl)amino]-3-oxo-3-piperazin-1-ylpropyl}benzenecarboximidamide
OpenEye OEToolkits 1.5.0 3-[(2S)-2-(naphthalen-2-ylsulfonylamino)-3-oxo-3-piperazin-1-yl-propyl]benzenecarboximidamide

Formula

C24 H27 N5 O3 S

Formal charge

0

Molecular weight

465.568 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N1CCNCC1)C(NS(=O)(=O)c3cc2ccccc2cc3)Cc4cc(C(=[N@H])N)ccc4
SMILES CACTVS 3.341 NC(=N)c1cccc(C[CH](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N4CCNCC4)c1
SMILES OpenEye OEToolkits 1.5.0 [H]N=C(c1cccc(c1)CC(C(=O)N2CCNCC2)NS(=O)(=O)c3ccc4ccccc4c3)N
Canonical SMILES CACTVS 3.341 NC(=N)c1cccc(C[C@H](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N4CCNCC4)c1
Canonical SMILES OpenEye OEToolkits 1.5.0 [H]/N=C(/c1cccc(c1)C[C@@H](C(=O)N2CCNCC2)NS(=O)(=O)c3ccc4ccccc4c3)\N

IUPAC InChI

InChI=1S/C24H27N5O3S/c25-23(26)20-7-3-4-17(14-20)15-22(24(30)29-12-10-27-11-13-29)28-33(31,32)21-9-8-18-5-1-2-6-19(18)16-21/h1-9,14,16,22,27-28H,10-13,15H2,(H3,25,26)/t22-/m0/s1

IUPAC InChI key

ZVDMTWWOKZXJOE-QFIPXVFZSA-N
FD3

wwPDB Information

Atom count

60 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-10-19

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



FD3 : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C65 C C65 N Y N 0 -0.606 0.814 2.96
2 C66 C C66 N Y N 0 -0.634 -0.502 3.369
3 C64 C C64 N Y N 0 0.221 1.721 3.597
4 C63 C C63 N Y N 0 1.019 1.316 4.652
5 C62 C C62 N Y N 0 0.994 0.003 5.074
6 C61 C C61 N Y N 0 0.162 -0.916 4.436
7 C25 C C25 N N N 0 0.131 -2.327 4.884
8 N43 N N43 N N N 0 0.924 -2.733 5.935
9 N54 N N54 N N N 0 -0.646 -3.183 4.286
10 C34 C C34 N N N 0 -1.473 1.265 1.812
11 C31 C C31 S N N 0 -0.706 1.099 0.499
12 C35 C C35 N N N 0 -1.573 1.549 -0.648
13 O36 O O36 N N N 0 -1.519 2.698 -1.035
14 N81 N N81 N N N 0 -2.408 0.676 -1.244
15 C71 C C71 N N N 0 -2.576 -0.69 -0.724
16 C72 C C72 N N N 0 -4.075 -0.982 -0.606
17 C74 C C74 N N N 0 -4.645 0.658 -2.211
18 C75 C C75 N N N 0 -3.187 1.06 -2.432
19 N40 N N40 N N N 0 -4.721 -0.774 -1.907
20 N29 N N29 N N N 0 0.511 1.912 0.539
21 S12 S S12 N N N 0 1.982 1.215 0.233
22 O32 O O32 N N N 0 2.913 2.288 0.178
23 O33 O O33 N N N 0 2.068 0.096 1.105
24 C2 C C2 N Y N 0 1.921 0.549 -1.396
25 C3 C C3 N Y N 0 2.304 1.343 -2.476
26 C4 C C4 N Y N 0 2.269 0.859 -3.748
27 C9 C C9 N Y N 0 1.452 -1.265 -2.88
28 C10 C C10 N Y N 0 1.841 -0.458 -3.979
29 C1 C C1 N Y N 0 1.507 -0.733 -1.581
30 C5 C C5 N Y N 0 1.791 -0.993 -5.277
31 C6 C C6 N Y N 0 1.372 -2.275 -5.463
32 C7 C C7 N Y N 0 0.989 -3.068 -4.383
33 C8 C C8 N Y N 0 1.024 -2.584 -3.111
34 H661 H 1H66 N N N 0 -1.281 -1.21 2.871
35 H641 H 1H64 N N N 0 0.244 2.75 3.27
36 H631 H 1H63 N N N 0 1.663 2.029 5.145
37 H621 H 1H62 N N N 0 1.618 -0.312 5.898
38 H431 H 1H43 N N N 0 0.904 -3.658 6.229
39 H432 H 2H43 N N N 0 1.507 -2.097 6.378
40 H541 H 1H54 N N N 0 -1.205 -2.897 3.547
41 H341 H 1H34 N N N 0 -2.379 0.66 1.783
42 H342 H 2H34 N N N 0 -1.739 2.313 1.948
43 H311 H 1H31 N N N 0 -0.439 0.051 0.363
44 H711 H 1H71 N N N 0 -2.116 -1.402 -1.41
45 H712 H 2H71 N N N 0 -2.107 -0.769 0.256
46 H721 H 1H72 N N N 0 -4.22 -2.015 -0.289
47 H722 H 2H72 N N N 0 -4.518 -0.311 0.13
48 H741 H 1H74 N N N 0 -5.221 0.87 -3.112
49 H742 H 2H74 N N N 0 -5.053 1.229 -1.377
50 H751 H 1H75 N N N 0 -3.122 2.138 -2.583
51 H752 H 2H75 N N N 0 -2.792 0.543 -3.307
52 H401 H 1H40 N N N 0 -5.698 -0.993 -1.784
53 H291 H 1H29 N N N 0 0.456 2.859 0.744
54 H31 H 1H3 N N N 0 2.633 2.357 -2.302
55 H41 H 1H4 N N N 0 2.568 1.486 -4.575
56 H11 H 1H1 N N N 0 1.218 -1.337 -0.734
57 H51 H 1H5 N N N 0 2.085 -0.39 -6.124
58 H61 H 1H6 N N N 0 1.335 -2.683 -6.462
59 H71 H 1H7 N N N 0 0.66 -4.081 -4.557
60 H81 H 1H8 N N N 0 0.724 -3.21 -2.284



FD3 : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C65 C66 C C doub 1.38 N Y
2 C65 C64 C C sing 1.38 N Y
3 C65 C34 C C sing 1.51 N N
4 C66 C61 C C sing 1.39 N Y
5 C66 H661 C H sing 1.08 N N
6 C64 C63 C C doub 1.38 N Y
7 C64 H641 C H sing 1.08 N N
8 C63 C62 C C sing 1.38 N Y
9 C63 H631 C H sing 1.08 N N
10 C62 C61 C C doub 1.39 N Y
11 C62 H621 C H sing 1.08 N N
12 C61 C25 C C sing 1.48 N N
13 C25 N43 C N sing 1.38 N N
14 C25 N54 C N doub 1.3 Z N
15 N43 H431 N H sing 0.97 N N
16 N43 H432 N H sing 0.97 N N
17 N54 H541 N H sing 0.97 N N
18 C34 C31 C C sing 1.53 N N
19 C34 H341 C H sing 1.09 N N
20 C34 H342 C H sing 1.09 N N
21 C31 C35 C C sing 1.51 N N
22 C31 N29 C N sing 1.46 N N
23 C31 H311 C H sing 1.09 N N
24 C35 O36 C O doub 1.21 N N
25 C35 N81 C N sing 1.35 N N
26 N81 C71 N C sing 1.47 N N
27 N81 C75 N C sing 1.47 N N
28 C71 C72 C C sing 1.53 N N
29 C71 H711 C H sing 1.09 N N
30 C71 H712 C H sing 1.09 N N
31 C72 N40 C N sing 1.47 N N
32 C72 H721 C H sing 1.09 N N
33 C72 H722 C H sing 1.09 N N
34 C74 C75 C C sing 1.53 N N
35 C74 N40 C N sing 1.47 N N
36 C74 H741 C H sing 1.09 N N
37 C74 H742 C H sing 1.09 N N
38 C75 H751 C H sing 1.09 N N
39 C75 H752 C H sing 1.09 N N
40 N40 H401 N H sing 1.01 N N
41 N29 S12 N S sing 1.66 N N
42 N29 H291 N H sing 0.97 N N
43 S12 O32 S O doub 1.42 N N
44 S12 O33 S O doub 1.42 N N
45 S12 C2 S C sing 1.76 N N
46 C2 C3 C C doub 1.39 N Y
47 C2 C1 C C sing 1.36 N Y
48 C3 C4 C C sing 1.36 N Y
49 C3 H31 C H sing 1.08 N N
50 C4 C10 C C doub 1.4 N Y
51 C4 H41 C H sing 1.08 N N
52 C9 C10 C C sing 1.42 N Y
53 C9 C1 C C doub 1.4 N Y
54 C9 C8 C C sing 1.41 N Y
55 C10 C5 C C sing 1.4 N Y
56 C1 H11 C H sing 1.08 N N
57 C5 C6 C C doub 1.36 N Y
58 C5 H51 C H sing 1.08 N N
59 C6 C7 C C sing 1.39 N Y
60 C6 H61 C H sing 1.08 N N
61 C7 C8 C C doub 1.36 N Y
62 C7 H71 C H sing 1.08 N N
63 C8 H81 C H sing 1.08 N N



FD3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
FD3 1k1l Open in New Window Bound ligand 1 1