Chemical Components in the PDB

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SPM : Summary

Code

SPM

One-letter code

X

Molecule name

SPERMINE

Systematic names

ProgramVersionName
ACDLabs 10.04 N,N'-bis(3-aminopropyl)butane-1,4-diamine
OpenEye OEToolkits 1.5.0 N,N'-bis(3-aminopropyl)butane-1,4-diamine

Formula

C10 H26 N4

Formal charge

0

Molecular weight

202.34 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 NCCCNCCCCNCCCN
SMILES CACTVS 3.341 NCCCNCCCCNCCCN
SMILES OpenEye OEToolkits 1.5.0 C(CCNCCCN)CNCCCN
Canonical SMILES CACTVS 3.341 NCCCNCCCCNCCCN
Canonical SMILES OpenEye OEToolkits 1.5.0 C(CCNCCCN)CNCCCN

IUPAC InChI

InChI=1S/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2

IUPAC InChI key

PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPM

wwPDB Information

Atom count

40 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAI

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



SPM : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C11 N N N 0 -0.433 0.0050 -4.237
2 C12 C C12 N N N 0 0.407 -0.032 -5.515
3 C13 C C13 N N N 0 -0.515 0.0050 -6.734
4 C2 C C2 N N N 0 0.514 -0.023 6.734
5 C3 C C3 N N N 0 -0.408 0.014 5.515
6 C4 C C4 N N N 0 0.432 -0.022 4.237
7 C6 C C6 N N N 0 0.411 -0.024 1.88
8 C7 C C7 N N N 0 -0.451 0.011 0.617
9 C8 C C8 N N N 0 0.45 -0.028 -0.617
10 C9 C C9 N N N 0 -0.412 0.0060 -1.88
11 H111 H 1H11 N N N 0 -1.099 -0.857 -4.215
12 H112 H 2H11 N N N 0 -1.023 0.921 -4.217
13 H121 H 1H12 N N N 0 1.074 0.83 -5.536
14 H122 H 2H12 N N N 0 0.998 -0.948 -5.534
15 H131 H 1H13 N N N 0 -1.181 -0.856 -6.713
16 H132 H 2H13 N N N 0 -1.105 0.921 -6.714
17 H21 H 1H2 N N N 0 1.181 0.838 6.713
18 H22 H 2H2 N N N 0 1.105 -0.939 6.715
19 H31 H 1H3 N N N 0 -1.074 -0.847 5.536
20 H32 H 2H3 N N N 0 -0.999 0.93 5.534
21 H41 H 1H4 N N N 0 1.098 0.839 4.215
22 H42 H 2H4 N N N 0 1.023 -0.938 4.217
23 H61 H 1H6 N N N 0 1.078 0.838 1.889
24 H62 H 2H6 N N N 0 1.002 -0.94 1.891
25 H71 H 1H7 N N N 0 -1.117 -0.851 0.608
26 H72 H 2H7 N N N 0 -1.042 0.927 0.607
27 H81 H 1H8 N N N 0 1.117 0.833 -0.608
28 H82 H 2H8 N N N 0 1.041 -0.944 -0.607
29 H91 H 1H9 N N N 0 -1.079 -0.855 -1.889
30 H92 H 2H9 N N N 0 -1.003 0.922 -1.891
31 HN0 H HN0 N N N 0 0.976 0.831 -3.071
32 HN11 H 1HN1 N N N 0 -0.739 0.916 7.988
33 HN12 H 2HN1 N N N 0 0.354 -0.014 8.735
34 HN41 H 1HN4 N N N 0 -0.354 -0.0030 -8.735
35 HN42 H 2HN4 N N N 0 0.814 0.833 -7.99
36 HN5 H HN5 N N N 0 -0.976 -0.849 3.071
37 N1 N N1 N N N 0 -0.292 0.012 7.961
38 N10 N N10 N N N 0 0.453 -0.031 -3.066
39 N14 N N14 N N N 0 0.292 -0.029 -7.961
40 N5 N N5 N N N 0 -0.453 0.013 3.066



SPM : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.47 N N
2 N1 HN11 N H sing 1.01 N N
3 N1 HN12 N H sing 1.01 N N
4 C2 C3 C C sing 1.53 N N
5 C2 H21 C H sing 1.09 N N
6 C2 H22 C H sing 1.09 N N
7 C3 C4 C C sing 1.53 N N
8 C3 H31 C H sing 1.09 N N
9 C3 H32 C H sing 1.09 N N
10 C4 N5 C N sing 1.47 N N
11 C4 H41 C H sing 1.09 N N
12 C4 H42 C H sing 1.09 N N
13 N5 C6 N C sing 1.47 N N
14 N5 HN5 N H sing 1.01 N N
15 C6 C7 C C sing 1.53 N N
16 C6 H61 C H sing 1.09 N N
17 C6 H62 C H sing 1.09 N N
18 C7 C8 C C sing 1.53 N N
19 C7 H71 C H sing 1.09 N N
20 C7 H72 C H sing 1.09 N N
21 C8 C9 C C sing 1.53 N N
22 C8 H81 C H sing 1.09 N N
23 C8 H82 C H sing 1.09 N N
24 C9 N10 C N sing 1.47 N N
25 C9 H91 C H sing 1.09 N N
26 C9 H92 C H sing 1.09 N N
27 N10 C11 N C sing 1.47 N N
28 N10 HN0 N H sing 1.01 N N
29 C11 C12 C C sing 1.53 N N
30 C11 H111 C H sing 1.09 N N
31 C11 H112 C H sing 1.09 N N
32 C12 C13 C C sing 1.53 N N
33 C12 H121 C H sing 1.09 N N
34 C12 H122 C H sing 1.09 N N
35 C13 N14 C N sing 1.47 N N
36 C13 H131 C H sing 1.09 N N
37 C13 H132 C H sing 1.09 N N
38 N14 HN41 N H sing 1.01 N N
39 N14 HN42 N H sing 1.01 N N



SPM : Used in PDB Entries

Total Number of PDB Entries: 165
Ligand Code PDB Entry ID Type Total Distinct
SPM 100d Open in New Window Bound ligand 1 1
SPM 131d Open in New Window Bound ligand 2 1
SPM 198d Open in New Window Bound ligand 1 1
SPM 1d10 Open in New Window Bound ligand 1 1
SPM 1d12 Open in New Window Bound ligand 1 1
SPM 1d15 Open in New Window Bound ligand 1 1
SPM 1d48 Open in New Window Bound ligand 1 1
SPM 1dcr Open in New Window Bound ligand 1 1
SPM 1dns Open in New Window Bound ligand 1 1
SPM 1dpl Open in New Window Bound ligand 2 1
SPM 1edr Open in New Window Bound ligand 1 1
SPM 1ei4 Open in New Window Bound ligand 1 1
SPM 1evv Open in New Window Bound ligand 1 1
SPM 1f6c Open in New Window Bound ligand 2 1
SPM 1fq2 Open in New Window Bound ligand 1 1
SPM 1fuf Open in New Window Bound ligand 1 1
SPM 1i0t Open in New Window Bound ligand 1 1
SPM 1i1p Open in New Window Bound ligand 1 1
SPM 1i2y Open in New Window Bound ligand 1 1
SPM 1ick Open in New Window Bound ligand 1 1
SPM 1j8g Open in New Window Bound ligand 1 1
SPM 1m69 Open in New Window Bound ligand 1 1
SPM 1n7a Open in New Window Bound ligand 2 1
SPM 1n7b Open in New Window Bound ligand 2 1
SPM 1ofx Open in New Window Bound ligand 1 1
SPM 1pwf Open in New Window Bound ligand 1 1
SPM 1rff Open in New Window Bound ligand 2 1
SPM 1rfi Open in New Window Bound ligand 1 1
SPM 1rg1 Open in New Window Bound ligand 1 1
SPM 1rg2 Open in New Window Bound ligand 1 1
SPM 1rgt Open in New Window Bound ligand 1 1
SPM 1rgu Open in New Window Bound ligand 1 1
SPM 1rh0 Open in New Window Bound ligand 1 1
SPM 1s2r Open in New Window Bound ligand 2 1
SPM 1tn1 Open in New Window Bound ligand 1 1
SPM 1tn2 Open in New Window Bound ligand 1 1
SPM 1vro Open in New Window Bound ligand 1 1
SPM 1woe Open in New Window Bound ligand 1 1
SPM 1xl6 Open in New Window Bound ligand 1 1
SPM 1xpf Open in New Window Bound ligand 1 1
SPM 1xpq Open in New Window Bound ligand 4 1
SPM 1y84 Open in New Window Bound ligand 1 1
SPM 1y8l Open in New Window Bound ligand 1 1
SPM 1yb9 Open in New Window Bound ligand 1 1
SPM 1z5t Open in New Window Bound ligand 2 1
SPM 1z7i Open in New Window Bound ligand 1 1
SPM 206d Open in New Window Bound ligand 2 1
SPM 210d Open in New Window Bound ligand 1 1
SPM 211d Open in New Window Bound ligand 1 1
SPM 248d Open in New Window Bound ligand 2 1
SPM 258d Open in New Window Bound ligand 1 1
SPM 2b2b Open in New Window Bound ligand 1 1
SPM 2b8j Open in New Window Bound ligand 1 1
SPM 2c12 Open in New Window Bound ligand 4 1
SPM 2d47 Open in New Window Bound ligand 1 1
SPM 2dcg Open in New Window Bound ligand 2 1
SPM 2f8w Open in New Window Bound ligand 1 1
SPM 2gun Open in New Window Bound ligand 1 1
SPM 2gwa Open in New Window Bound ligand 1 1
SPM 2o3y Open in New Window Bound ligand 1 1
SPM 2pl8 Open in New Window Bound ligand 1 1
SPM 2plb Open in New Window Bound ligand 1 1
SPM 2rf3 Open in New Window Bound ligand 1 1
SPM 2tra Open in New Window Bound ligand 1 1
SPM 2wlj Open in New Window Bound ligand 1 1
SPM 2wlk Open in New Window Bound ligand 1 1
SPM 320d Open in New Window Bound ligand 1 1
SPM 321d Open in New Window Bound ligand 2 1
SPM 323d Open in New Window Bound ligand 1 1
SPM 324d Open in New Window Bound ligand 2 1
SPM 326d Open in New Window Bound ligand 1 1
SPM 355d Open in New Window Bound ligand 1 1
SPM 3b7p Open in New Window Bound ligand 3 1
SPM 3bj8 Open in New Window Bound ligand 1 1
SPM 3c6m Open in New Window Bound ligand 4 1
SPM 3eui Open in New Window Bound ligand 1 1
SPM 3ku9 Open in New Window Bound ligand 2 1
SPM 3kwa Open in New Window Bound ligand 1 1
SPM 3lp9 Open in New Window Bound ligand 1 1
SPM 3oz5 Open in New Window Bound ligand 1 1
SPM 3p4j Open in New Window Bound ligand 1 1
SPM 3qj7 Open in New Window Bound ligand 1 1
SPM 3tzo Open in New Window Bound ligand 1 1
SPM 3vkg Open in New Window Bound ligand 4 1
SPM 410d Open in New Window Bound ligand 1 1
SPM 428d Open in New Window Bound ligand 1 1
SPM 4e8k Open in New Window Bound ligand 1 1
SPM 4e8m Open in New Window Bound ligand 2 1
SPM 4e8n Open in New Window Bound ligand 1 1
SPM 4e8p Open in New Window Bound ligand 1 1
SPM 4e8q Open in New Window Bound ligand 1 1
SPM 4e8t Open in New Window Bound ligand 2 1
SPM 4faq Open in New Window Bound ligand 2 1
SPM 4far Open in New Window Bound ligand 2 1
SPM 4fau Open in New Window Bound ligand 1 1
SPM 4faw Open in New Window Bound ligand 1 1
SPM 4fb0 Open in New Window Bound ligand 1 1
SPM 4hqi Open in New Window Bound ligand 1 1
SPM 4mi4 Open in New Window Bound ligand 3 1
SPM 4mj8 Open in New Window Bound ligand 4 1
SPM 4nfo Open in New Window Bound ligand 1 1
SPM 4p5j Open in New Window Bound ligand 1 1
SPM 4r0d Open in New Window Bound ligand 2 1
SPM 4r4a Open in New Window Bound ligand 1 1
SPM 4r87 Open in New Window Bound ligand 6 1
SPM 5de9 Open in New Window Bound ligand 1 1
SPM 5ob3 Open in New Window Bound ligand 1 1
SPM 5v1l Open in New Window Bound ligand 1 1
SPM 5vj9 Open in New Window Bound ligand 5 1
SPM 5vjb Open in New Window Bound ligand 4 1
SPM 5xjz Open in New Window Bound ligand 1 1
SPM 6af2 Open in New Window Bound ligand 3 1
SPM 6chr Open in New Window Bound ligand 1 1
SPM 6e1x Open in New Window Bound ligand 6 1
SPM 6e8s Open in New Window Bound ligand 1 1
SPM 6gaw Open in New Window Bound ligand 3 1
SPM 6gaz Open in New Window Bound ligand 1 1
SPM 6gb2 Open in New Window Bound ligand 2 1
SPM 6gda Open in New Window Bound ligand 2 1
SPM 6hiv Open in New Window Bound ligand 1 1
SPM 6hiw Open in New Window Bound ligand 1 1
SPM 6hiy Open in New Window Bound ligand 1 1
SPM 6rsj Open in New Window Bound ligand 2 1
SPM 6rsk Open in New Window Bound ligand 4 1
SPM 6rsl Open in New Window Bound ligand 8 1
SPM 6rw4 Open in New Window Bound ligand 1 1
SPM 6rw5 Open in New Window Bound ligand 1 1
SPM 6s7d Open in New Window Bound ligand 1 1
SPM 6t3k Open in New Window Bound ligand 2 1
SPM 6t3r Open in New Window Bound ligand 2 1
SPM 6uej Open in New Window Bound ligand 1 1
SPM 6vfn Open in New Window Bound ligand 12 1
SPM 6xt7 Open in New Window Bound ligand 2 1
SPM 6xxl Open in New Window Bound ligand 2 1
SPM 6ydp Open in New Window Bound ligand 3 1
SPM 6ydw Open in New Window Bound ligand 3 1
SPM 6yec Open in New Window Bound ligand 2 1
SPM 6ywe Open in New Window Bound ligand 1 1
SPM 6yws Open in New Window Bound ligand 1 1
SPM 6ywv Open in New Window Bound ligand 1 1
SPM 6ywx Open in New Window Bound ligand 1 1
SPM 6ywy Open in New Window Bound ligand 1 1
SPM 7d5d Open in New Window Bound ligand 2 1
SPM 7d5e Open in New Window Bound ligand 4 1
SPM 7k00 Open in New Window Bound ligand 1 1
SPM 7ky3 Open in New Window Bound ligand 3 1
SPM 7ky4 Open in New Window Bound ligand 4 1
SPM 7l0z Open in New Window Bound ligand 3 1
SPM 7n72 Open in New Window Bound ligand 1 1
SPM 7n78 Open in New Window Bound ligand 1 1
SPM 7ne4 Open in New Window Bound ligand 3 1
SPM 7ne5 Open in New Window Bound ligand 2 1
SPM 7ne7 Open in New Window Bound ligand 6 1
SPM 7nqh Open in New Window Bound ligand 3 1
SPM 7nql Open in New Window Bound ligand 3 1
SPM 7nsh Open in New Window Bound ligand 2 1
SPM 7nsi Open in New Window Bound ligand 3 1
SPM 7nsj Open in New Window Bound ligand 3 1
SPM 7o7y Open in New Window Bound ligand 3 1
SPM 7o7z Open in New Window Bound ligand 3 1
SPM 7oaw Open in New Window Bound ligand 1 1
SPM 7oax Open in New Window Bound ligand 4 1
SPM 7ob1 Open in New Window Bound ligand 5 1
SPM 7op1 Open in New Window Bound ligand 1 1
SPM 7op3 Open in New Window Bound ligand 1 1