Chemical Components in the PDB

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T09 : Summary

Code

T09

One-letter code

X

Molecule name

(2S,4R)-2-amino-4-methyloctanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S,4R)-2-amino-4-methyloctanoic acid
OpenEye OEToolkits 2.0.7 (2~{S},4~{R})-2-azanyl-4-methyl-octanoic acid

Formula

C9 H19 N O2

Formal charge

0

Molecular weight

173.253 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NC(CC(C)CCCC)C(=O)O
SMILES CACTVS 3.385 CCCC[CH](C)C[CH](N)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 CCCCC(C)CC(C(=O)O)N
Canonical SMILES CACTVS 3.385 CCCC[C@@H](C)C[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCC[C@@H](C)C[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C9H19NO2/c1-3-4-5-7(2)6-8(10)9(11)12/h7-8H,3-6,10H2,1-2H3,(H,11,12)/t7-,8+/m1/s1

IUPAC InChI key

YPMMOCARISFQBS-SFYZADRCSA-N
T09

wwPDB Information

Atom count

31 (12 without Hydrogen)

Polymer type

Amino Acid

Type description

L-peptide linking

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2022-07-13

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



T09 : Atoms of Molecule

Total Number of Atoms: 31
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 5.543 0.211 0.093
2 C02 C C02 N N N 0 4.24 -0.172 0.797
3 C03 C C03 N N N 0 3.055 0.139 -0.12
4 C04 C C04 N N N 0 1.751 -0.244 0.584
5 C05 C C05 R N N 0 0.566 0.066 -0.332
6 C06 C C06 N N N 0 -0.741 -0.199 0.417
7 CA C C07 S N N 0 -1.924 0.228 -0.454
8 C C C08 N N N 0 -3.213 -0.145 0.231
9 C67 C C67 N N N 0 0.633 -0.827 -1.573
10 N N N N N N 0 -1.881 1.683 -0.658
11 O O O66 N N N 0 -3.839 0.692 0.837
12 OXT O OXT N N Y 0 -3.666 -1.407 0.167
13 H011 H H011 N N N 0 5.639 -0.36 -0.831
14 H012 H H012 N N N 0 5.532 1.276 -0.139
15 H013 H H013 N N N 0 6.387 -0.01 0.746
16 H021 H H021 N N N 0 4.251 -1.237 1.028
17 H022 H H022 N N N 0 4.144 0.399 1.72
18 H031 H H031 N N N 0 3.043 1.204 -0.351
19 H032 H H032 N N N 0 3.15 -0.433 -1.043
20 H042 H H042 N N N 0 1.763 -1.309 0.816
21 H041 H H041 N N N 0 1.656 0.327 1.508
22 H051 H H051 N N N 0 0.606 1.112 -0.635
23 H062 H H062 N N N 0 -0.821 -1.263 0.642
24 H061 H H061 N N N 0 -0.749 0.37 1.346
25 HA H H071 N N N 0 -1.866 -0.276 -1.419
26 H672 H H672 N N N 0 -0.211 -0.606 -2.226
27 H671 H H671 N N N 0 1.565 -0.638 -2.106
28 H673 H H673 N N N 0 0.594 -1.873 -1.27
29 H2 H H2 N N Y 0 -1.934 2.173 0.222
30 H H H N N N 0 -1.056 1.951 -1.173
31 HXT H HXT N N Y 0 -4.497 -1.599 0.622



T09 : Chemical Bonds

Total Number of Bonds: 30
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C67 C05 C C sing 1.53 N N
2 C CA C C sing 1.51 N N
3 C O C O doub 1.21 N N
4 C06 CA C C sing 1.53 N N
5 C06 C05 C C sing 1.53 N N
6 CA N C N sing 1.47 N N
7 C05 C04 C C sing 1.53 N N
8 C04 C03 C C sing 1.53 N N
9 C03 C02 C C sing 1.53 N N
10 C02 C01 C C sing 1.53 N N
11 C OXT C O sing 1.34 N N
12 C01 H011 C H sing 1.09 N N
13 C01 H012 C H sing 1.09 N N
14 C01 H013 C H sing 1.09 N N
15 C02 H021 C H sing 1.09 N N
16 C02 H022 C H sing 1.09 N N
17 C03 H031 C H sing 1.09 N N
18 C03 H032 C H sing 1.09 N N
19 C04 H042 C H sing 1.09 N N
20 C04 H041 C H sing 1.09 N N
21 C05 H051 C H sing 1.09 N N
22 C06 H062 C H sing 1.09 N N
23 C06 H061 C H sing 1.09 N N
24 CA HA C H sing 1.09 N N
25 C67 H672 C H sing 1.09 N N
26 C67 H671 C H sing 1.09 N N
27 C67 H673 C H sing 1.09 N N
28 N H2 N H sing 1.01 N N
29 N H N H sing 1.01 N N
30 OXT HXT O H sing 0.97 N N



T09 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
T09 8dnx Open in New Window Polymer component 1 1