Chemical Components in the PDB

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5H3 : Summary

Code

5H3

One-letter code

X

Molecule name

N-[3-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[3-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide
OpenEye OEToolkits 1.7.6 N-[3-[[2-(3-fluorophenyl)ethylamino]methyl]phenyl]thiophene-2-carboximidamide

Formula

C20 H20 F N3 S

Formal charge

0

Molecular weight

353.456 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Fc1cccc(c1)CCNCc2cc(ccc2)NC(=[N@H])c3sccc3
SMILES CACTVS 3.370 Fc1cccc(CCNCc2cccc(NC(=N)c3sccc3)c2)c1
SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)F)CCNCc2cccc(c2)NC(=N)c3cccs3
Canonical SMILES CACTVS 3.370 Fc1cccc(CCNCc2cccc(NC(=N)c3sccc3)c2)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C(\c1cccs1)/Nc2cccc(c2)CNCCc3cccc(c3)F

IUPAC InChI

InChI=1S/C20H20FN3S/c21-17-6-1-4-15(12-17)9-10-23-14-16-5-2-7-18(13-16)24-20(22)19-8-3-11-25-19/h1-8,11-13,23H,9-10,14H2,(H2,22,24)

IUPAC InChI key

QJSHZJYEBIUVCD-UHFFFAOYSA-N
5H3

wwPDB Information

Atom count

45 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-04-26

Last modified at

2014-02-07

Status

Released

Obsoleted

Not Assigned



5H3 : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 F23 F F23 N N N 0 -8.468 -0.261 0.032
2 C23 C C23 N Y N 0 -7.361 0.513 0.006
3 C24 C C24 N Y N 0 -7.442 1.821 -0.44
4 C25 C C25 N Y N 0 -6.309 2.613 -0.467
5 C22 C C22 N Y N 0 -6.147 0.001 0.43
6 C21 C C21 N Y N 0 -5.015 0.794 0.402
7 C26 C C26 N Y N 0 -5.096 2.099 -0.048
8 C20 C C20 N N N 0 -3.694 0.236 0.864
9 C19 C C19 N N N 0 -2.966 -0.399 -0.323
10 N18 N N18 N N N 0 -1.677 -0.942 0.127
11 C17 C C17 N N N 0 -0.949 -1.561 -0.989
12 C15 C C15 N Y N 0 0.365 -2.106 -0.49
13 C14 C C14 N Y N 0 0.441 -3.405 -0.022
14 C13 C C13 N Y N 0 1.644 -3.909 0.437
15 C12 C C12 N Y N 0 2.774 -3.115 0.429
16 C16 C C16 N Y N 0 1.493 -1.309 -0.506
17 C11 C C11 N Y N 0 2.702 -1.81 -0.04
18 N07 N N07 N N N 0 3.844 -1.004 -0.049
19 C06 C C06 N N N 0 3.749 0.332 0.29
20 N08 N N08 N N N 0 2.618 0.815 0.732
21 C05 C C05 N Y N 0 4.921 1.211 0.154
22 S01 S S01 N Y N 0 6.505 0.714 -0.424
23 C02 C C02 N Y N 0 7.121 2.294 -0.234
24 C03 C C03 N Y N 0 6.181 3.121 0.233
25 C04 C C04 N Y N 0 4.95 2.541 0.45
26 H1 H H1 N N N 0 -8.389 2.223 -0.768
27 H2 H H2 N N N 0 -6.371 3.633 -0.815
28 H3 H H3 N N N 0 -6.084 -1.018 0.782
29 H4 H H4 N N N 0 -4.211 2.717 -0.07
30 H5 H H5 N N N 0 -3.084 1.041 1.276
31 H6 H H6 N N N 0 -3.865 -0.519 1.631
32 H7 H H7 N N N 0 -3.575 -1.203 -0.735
33 H8 H H8 N N N 0 -2.794 0.356 -1.09
34 H9 H H9 N N N 0 -1.805 -1.597 0.883
35 H11 H H11 N N N 0 -1.544 -2.374 -1.405
36 H12 H H12 N N N 0 -0.763 -0.814 -1.76
37 H13 H H13 N N N 0 -0.442 -4.028 -0.015
38 H14 H H14 N N N 0 1.7 -4.924 0.802
39 H15 H H15 N N N 0 3.714 -3.509 0.788
40 H16 H H16 N N N 0 1.434 -0.296 -0.876
41 H17 H H17 N N N 0 4.703 -1.382 -0.293
42 H18 H H18 N N N 0 1.872 0.22 0.908
43 H19 H H19 N N N 0 8.136 2.587 -0.461
44 H20 H H20 N N N 0 6.371 4.167 0.422
45 H21 H H21 N N N 0 4.096 3.085 0.825



5H3 : Chemical Bonds

Total Number of Bonds: 47
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C03 C02 C C doub 1.34 N Y
2 C03 C04 C C sing 1.38 N Y
3 C02 S01 C S sing 1.71 N Y
4 C04 C05 C C doub 1.36 N Y
5 S01 C05 S C sing 1.76 N Y
6 C05 C06 C C sing 1.47 N N
7 C06 N08 C N doub 1.31 N N
8 C06 N07 C N sing 1.38 N N
9 C12 C13 C C doub 1.38 N Y
10 C12 C11 C C sing 1.39 N Y
11 C13 C14 C C sing 1.38 N Y
12 N07 C11 N C sing 1.4 N N
13 C11 C16 C C doub 1.39 N Y
14 C14 C15 C C doub 1.38 N Y
15 C16 C15 C C sing 1.38 N Y
16 C15 C17 C C sing 1.51 N N
17 C17 N18 C N sing 1.47 N N
18 N18 C19 N C sing 1.47 N N
19 C19 C20 C C sing 1.53 N N
20 C26 C25 C C doub 1.38 N Y
21 C26 C21 C C sing 1.38 N Y
22 C25 C24 C C sing 1.38 N Y
23 C20 C21 C C sing 1.51 N N
24 C21 C22 C C doub 1.38 N Y
25 C24 C23 C C doub 1.38 N Y
26 C22 C23 C C sing 1.38 N Y
27 C23 F23 C F sing 1.35 N N
28 C24 H1 C H sing 1.08 N N
29 C25 H2 C H sing 1.08 N N
30 C22 H3 C H sing 1.08 N N
31 C26 H4 C H sing 1.08 N N
32 C20 H5 C H sing 1.09 N N
33 C20 H6 C H sing 1.09 N N
34 C19 H7 C H sing 1.09 N N
35 C19 H8 C H sing 1.09 N N
36 N18 H9 N H sing 1.01 N N
37 C17 H11 C H sing 1.09 N N
38 C17 H12 C H sing 1.09 N N
39 C14 H13 C H sing 1.08 N N
40 C13 H14 C H sing 1.08 N N
41 C12 H15 C H sing 1.08 N N
42 C16 H16 C H sing 1.08 N N
43 N07 H17 N H sing 0.97 N N
44 N08 H18 N H sing 0.97 N N
45 C02 H19 C H sing 1.08 N N
46 C03 H20 C H sing 1.08 N N
47 C04 H21 C H sing 1.08 N N



5H3 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5H3 4kcn Open in New Window Bound ligand 2 1
5H3 4kcr Open in New Window Bound ligand 2 1