Chemical Components in the PDB

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SP5 : Summary

Code

SP5

One-letter code

X

Molecule name

N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide
OpenEye OEToolkits 1.5.0 N-[3-[4-(3-aminopropylamino)butylamino]propyl]ethanamide

Formula

C12 H28 N4 O

Formal charge

0

Molecular weight

244.377 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NCCCNCCCCNCCCN)C
SMILES CACTVS 3.341 CC(=O)NCCCNCCCCNCCCN
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NCCCNCCCCNCCCN
Canonical SMILES CACTVS 3.341 CC(=O)NCCCNCCCCNCCCN
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)NCCCNCCCCNCCCN

IUPAC InChI

InChI=1S/C12H28N4O/c1-12(17)16-11-5-10-15-8-3-2-7-14-9-4-6-13/h14-15H,2-11,13H2,1H3,(H,16,17)

IUPAC InChI key

GUNURVWAJRRUAV-UHFFFAOYSA-N
SP5

wwPDB Information

Atom count

45 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-03-31

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



SP5 : 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 CAB C CAB N N N 0 8.749 -0.83 0.008
2 CAC C CAC N N N 0 7.533 0.06 0.0
3 OAA O OAA N N N 0 7.663 1.265 -0.011
4 NAD N NAD N N N 0 6.3 -0.485 0.006
5 CAE C CAE N N N 0 5.117 0.38 -0.002
6 CAF C CAF N N N 0 3.854 -0.484 0.007
7 CAG C CAG N N N 0 2.619 0.419 -0.002
8 NAH N NAH N N N 0 1.406 -0.41 0.007
9 CAI C CAI N N N 0 0.198 0.425 -0.001
10 CAJ C CAJ N N N 0 -1.042 -0.472 0.008
11 CAK C CAK N N N 0 -2.301 0.398 0.0
12 CAL C CAL N N N 0 -3.54 -0.499 0.009
13 NAM N NAM N N N 0 -4.749 0.336 0.002
14 CAN C CAN N N N 0 -5.961 -0.493 0.01
15 CAO C CAO N N N 0 -7.196 0.41 0.002
16 CAP C CAP N N N 0 -8.46 -0.454 0.01
17 NAQ N NAQ N N N 0 -9.645 0.413 0.002
18 HAB H HAB N N N 0 9.043 -1.034 1.038
19 HABA H HABA N N N 0 8.517 -1.767 -0.497
20 HABB H HABB N N N 0 9.568 -0.331 -0.511
21 HNAD H HNAD N N N 0 6.196 -1.449 0.015
22 HAE H HAE N N N 0 5.127 1.017 0.882
23 HAEA H HAEA N N N 0 5.127 1.0 -0.898
24 HAF H HAF N N N 0 3.844 -1.122 -0.877
25 HAFA H HAFA N N N 0 3.845 -1.105 0.902
26 HAG H HAG N N N 0 2.629 1.057 0.882
27 HAGA H HAGA N N N 0 2.629 1.04 -0.898
28 HNAH H HNAH N N N 0 1.405 -1.056 -0.769
29 HAI H HAI N N N 0 0.191 1.063 0.883
30 HAIA H HAIA N N N 0 0.191 1.046 -0.897
31 HAJ H HAJ N N N 0 -1.035 -1.11 -0.876
32 HAJA H HAJA N N N 0 -1.035 -1.092 0.904
33 HAK H HAK N N N 0 -2.307 1.036 0.884
34 HAKA H HAKA N N N 0 -2.308 1.019 -0.896
35 HAL H HAL N N N 0 -3.533 -1.137 -0.875
36 HALA H HALA N N N 0 -3.533 -1.12 0.905
37 HNAM H HNAM N N N 0 -4.747 0.982 0.777
38 HAN H HAN N N N 0 -5.972 -1.131 -0.874
39 HANA H HANA N N N 0 -5.971 -1.114 0.906
40 HAO H HAO N N N 0 -7.186 1.048 0.886
41 HAOA H HAOA N N N 0 -7.187 1.031 -0.894
42 HAP H HAP N N N 0 -8.47 -1.091 -0.874
43 HAPA H HAPA N N N 0 -8.469 -1.074 0.906
44 HNAQ H HNAQ N N N 0 -9.627 1.044 -0.785
45 HNAA H HNAA N N N 0 -10.493 -0.134 0.008



SP5 : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAB CAC C C sing 1.51 N N
2 CAC OAA C O doub 1.21 N N
3 CAC NAD C N sing 1.35 N N
4 NAD CAE N C sing 1.47 N N
5 CAE CAF C C sing 1.53 N N
6 CAF CAG C C sing 1.53 N N
7 CAG NAH C N sing 1.47 N N
8 NAH CAI N C sing 1.47 N N
9 CAI CAJ C C sing 1.53 N N
10 CAJ CAK C C sing 1.53 N N
11 CAK CAL C C sing 1.53 N N
12 CAL NAM C N sing 1.47 N N
13 NAM CAN N C sing 1.47 N N
14 CAN CAO C C sing 1.53 N N
15 CAO CAP C C sing 1.53 N N
16 CAP NAQ C N sing 1.47 N N
17 CAB HAB C H sing 1.09 N N
18 CAB HABA C H sing 1.09 N N
19 CAB HABB C H sing 1.09 N N
20 NAD HNAD N H sing 0.97 N N
21 CAE HAE C H sing 1.09 N N
22 CAE HAEA C H sing 1.09 N N
23 CAF HAF C H sing 1.09 N N
24 CAF HAFA C H sing 1.09 N N
25 CAG HAG C H sing 1.09 N N
26 CAG HAGA C H sing 1.09 N N
27 NAH HNAH N H sing 1.01 N N
28 CAI HAI C H sing 1.09 N N
29 CAI HAIA C H sing 1.09 N N
30 CAJ HAJ C H sing 1.09 N N
31 CAJ HAJA C H sing 1.09 N N
32 CAK HAK C H sing 1.09 N N
33 CAK HAKA C H sing 1.09 N N
34 CAL HAL C H sing 1.09 N N
35 CAL HALA C H sing 1.09 N N
36 NAM HNAM N H sing 1.01 N N
37 CAN HAN C H sing 1.09 N N
38 CAN HANA C H sing 1.09 N N
39 CAO HAO C H sing 1.09 N N
40 CAO HAOA C H sing 1.09 N N
41 CAP HAP C H sing 1.09 N N
42 CAP HAPA C H sing 1.09 N N
43 NAQ HNAQ N H sing 1.01 N N
44 NAQ HNAA N H sing 1.01 N N



SP5 : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
SP5 3cnd Open in New Window Bound ligand 1 1
SP5 3q9e Open in New Window Bound ligand 12 1
SP5 5lfo Open in New Window Bound ligand 1 1
SP5 5mbx Open in New Window Bound ligand 1 1
SP5 6e1x Open in New Window Bound ligand 3 1