Chemical Components in the PDB

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H5M : Summary

Code

H5M

One-letter code

P

Molecule name

TRANS-3-HYDROXY-5-METHYLPROLINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (3S,5S)-3-hydroxy-5-methyl-L-proline
OpenEye OEToolkits 1.5.0 (2S,3S,5S)-3-hydroxy-5-methyl-pyrrolidine-2-carboxylic acid

Formula

C6 H11 N O3

Formal charge

0

Molecular weight

145.156 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C1NC(C)CC1O
SMILES CACTVS 3.341 C[CH]1C[CH](O)[CH](N1)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC1CC(C(N1)C(=O)O)O
Canonical SMILES CACTVS 3.341 C[C@H]1C[C@H](O)[C@H](N1)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@H]1C[C@@H]([C@H](N1)C(=O)O)O

IUPAC InChI

InChI=1S/C6H11NO3/c1-3-2-4(8)5(7-3)6(9)10/h3-5,7-8H,2H2,1H3,(H,9,10)/t3-,4-,5-/m0/s1

IUPAC InChI key

RVIGBNHLNBRMFX-YUPRTTJUSA-N
H5M

wwPDB Information

Atom count

21 (10 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

PRO

Defined at

1999-07-08

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



H5M : Atoms of Molecule

Total Number of Atoms: 21
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 1.074 -0.489 0.678
2 CA C CA S N N 0 0.035 -0.519 -0.386
3 C C C N N N 0 0.583 0.011 -1.685
4 O O O N N N 0 1.526 0.767 -1.679
5 OXT O OXT N N Y 0 0.023 -0.354 -2.849
6 CB C CB S N N 0 -1.068 0.416 0.165
7 CG C CG N N N 0 -1.056 0.11 1.68
8 CD C CD S N N 0 0.335 -0.486 1.959
9 OB O OB N N N 0 -2.339 0.097 -0.404
10 CD1 C CD1 N N N 0 1.075 0.372 2.986
11 H H HN N N Y 0 1.569 -1.367 0.625
12 HA H HA N N N 0 -0.348 -1.531 -0.517
13 HXT H HXT N N Y 0 0.375 -0.013 -3.683
14 HB H HB N N N 0 -0.816 1.461 -0.018
15 HG2 H 1HG N N N 0 -1.834 -0.612 1.927
16 HG3 H 2HG N N N 0 -1.195 1.027 2.253
17 HD H HD N N N 0 0.234 -1.506 2.331
18 HOB H HOB N N N 0 -2.992 0.658 0.035
19 HD11 H 1HD1 N N N 0 2.061 -0.052 3.172
20 HD12 H 2HD1 N N N 0 1.183 1.386 2.601
21 HD13 H 3HD1 N N N 0 0.508 0.395 3.916



H5M : Chemical Bonds

Total Number of Bonds: 21
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.49 N N
2 N CD N C sing 1.48 N N
3 N H N H sing 1.01 N N
4 CA C C C sing 1.51 N N
5 CA CB C C sing 1.55 N N
6 CA HA C H sing 1.09 N N
7 C O C O doub 1.21 N N
8 C OXT C O sing 1.34 N N
9 OXT HXT O H sing 0.97 N N
10 CB CG C C sing 1.55 N N
11 CB OB C O sing 1.43 N N
12 CB HB C H sing 1.09 N N
13 CG CD C C sing 1.54 N N
14 CG HG2 C H sing 1.09 N N
15 CG HG3 C H sing 1.09 N N
16 CD CD1 C C sing 1.53 N N
17 CD HD C H sing 1.09 N N
18 OB HOB O H sing 0.97 N N
19 CD1 HD11 C H sing 1.09 N N
20 CD1 HD12 C H sing 1.09 N N
21 CD1 HD13 C H sing 1.09 N N



H5M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
H5M 1a7z Open in New Window Polymer component 2 1