Chemical Components in the PDB

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API : Summary

Code

API

One-letter code

K

Molecule name

2,6-DIAMINOPIMELIC ACID

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R,6S)-2,6-diaminoheptanedioic acid
OpenEye OEToolkits 1.7.2 (2S,6R)-2,6-bis(azanyl)heptanedioic acid

Formula

C7 H14 N2 O4

Formal charge

0

Molecular weight

190.197 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCCC(C(=O)O)N
SMILES CACTVS 3.370 N[CH](CCC[CH](N)C(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.2 C(CC(C(=O)O)N)CC(C(=O)O)N
Canonical SMILES CACTVS 3.370 N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.2 C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+

IUPAC InChI key

GMKMEZVLHJARHF-SYDPRGILSA-N
API

wwPDB Information

Atom count

27 (13 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

1999-07-08

Last modified at

2011-09-05

Status

Released

Obsoleted

Not Assigned



API : Atoms of Molecule

Total Number of Atoms: 27
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 3.726 -0.379 -0.101
2 C2 C C2 S N N 0 2.498 0.269 0.486
3 C3 C C3 N N N 0 1.249 -0.295 -0.194
4 C4 C C4 N N N 0 0.0 0.269 0.486
5 C5 C C5 N N N 0 -1.25 -0.295 -0.193
6 C6 C C6 R N N 0 -2.499 0.269 0.486
7 C7 C C7 N N N 0 -3.726 -0.379 -0.1
8 H2 H H2 N N Y 0 2.455 0.063 1.555
9 H31 H H31 N N N 0 1.249 -0.012 -1.246
10 H32 H H32 N N N 0 1.249 -1.382 -0.109
11 H41 H H41 N N N 0 0.0 -0.013 1.539
12 H42 H H42 N N N 0 0.0 1.356 0.402
13 H51 H H51 N N N 0 -1.25 -0.012 -1.246
14 H52 H H52 N N N 0 -1.25 -1.382 -0.109
15 H6 H H6 N N N 0 -2.455 0.063 1.556
16 HN21 H HN21 N N N 0 2.601 1.938 -0.715
17 HN22 H HN22 N N N 0 1.781 2.186 0.71
18 HN61 H HN61 N N N 0 -1.781 2.186 0.711
19 HN62 H HN62 N N N 0 -2.602 1.939 -0.714
20 HO2 H HO2 N N N 0 4.895 -1.975 -0.096
21 HO4 H HO4 N N N 0 -4.893 -1.977 -0.098
22 N2 N N2 N N N 0 2.56 1.721 0.269
23 N6 N N6 N N N 0 -2.56 1.721 0.27
24 O1 O O1 N N N 0 4.374 0.203 -0.938
25 O2 O O2 N N Y 0 4.101 -1.6 0.309
26 O3 O O3 N N N 0 -4.375 0.203 -0.937
27 O4 O O4 N N Y 0 -4.098 -1.602 0.307



API : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C1 O1 C O doub 1.21 N N
3 C1 O2 C O sing 1.34 N N
4 C2 C3 C C sing 1.53 N N
5 C2 N2 C N sing 1.47 N N
6 C2 H2 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 C5 C C sing 1.53 N N
11 C4 H41 C H sing 1.09 N N
12 C4 H42 C H sing 1.09 N N
13 C5 C6 C C sing 1.53 N N
14 C5 H51 C H sing 1.09 N N
15 C5 H52 C H sing 1.09 N N
16 C6 C7 C C sing 1.51 N N
17 C6 N6 C N sing 1.47 N N
18 C6 H6 C H sing 1.09 N N
19 C7 O3 C O doub 1.21 N N
20 C7 O4 C O sing 1.34 N N
21 O2 HO2 O H sing 0.97 N N
22 O4 HO4 O H sing 0.97 N N
23 N2 HN21 N H sing 1.01 N N
24 N2 HN22 N H sing 1.01 N N
25 N6 HN61 N H sing 1.01 N N
26 N6 HN62 N H sing 1.01 N N



API : Used in PDB Entries

Total Number of PDB Entries: 33
Ligand Code PDB Entry ID Type Total Distinct
API 148l Open in New Window Polymer component 1 1
API 1e8c Open in New Window Bound ligand 2 1
API 2dap Open in New Window Bound ligand 1 1
API 2mtz Open in New Window Polymer component 6 1
API 3td4 Open in New Window Bound ligand 8 1
API 3td5 Open in New Window Polymer component 8 1
API 3vdf Open in New Window Bound ligand 1 1
API 3wbf Open in New Window Bound ligand 3 1
API 3wgq Open in New Window Bound ligand 1 1
API 4bxe Open in New Window Polymer component 2 1
API 4chx Open in New Window Polymer component 1 1
API 4cvk Open in New Window Bound ligand 1 1
API 4g4v Open in New Window Bound ligand 1 1
API 4g88 Open in New Window Bound ligand 8 1
API 4q6o Open in New Window Bound ligand 1 1
API 4q6p Open in New Window Bound ligand 1 1
API 4q6q Open in New Window Bound ligand 1 1
API 4wck Open in New Window Bound ligand 1 1
API 4wcl Open in New Window Bound ligand 1 1
API 4wcm Open in New Window Bound ligand 1 1
API 4wkm Open in New Window Polymer component 8 1
API 5aa1 Open in New Window Polymer component 1 1
API 5aa2 Open in New Window Polymer component 1 1
API 5lkw Open in New Window Bound ligand 2 1
API 5m3g Open in New Window Bound ligand 1 1
API 5m47 Open in New Window Bound ligand 1 1
API 5vo3 Open in New Window Bound ligand 1 1
API 6a89 Open in New Window Bound ligand 1 1
API 6fbt Open in New Window Polymer component 1 1
API 6fcr Open in New Window Polymer component 2 1
API 6fcs Open in New Window Polymer component 1 1
API 6jn0 Open in New Window Polymer component 1 1
API 6v40 Open in New Window Bound ligand 4 1