Chemical Components in the PDB

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TLP : Summary

Code

TLP

One-letter code

X

Molecule name

3-HYDROXY-2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-BUTYRIC ACID

Synonyms

N-PYRIDOXYL-THREONINE-5-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)threonine
OpenEye OEToolkits 1.5.0 3-hydroxy-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]butanoic acid

Formula

C12 H19 N2 O8 P

Formal charge

0

Molecular weight

350.262 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)C(O)C
SMILES CACTVS 3.341 CC(O)C(NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C(C)O)C(=O)O)O
Canonical SMILES CACTVS 3.341 CC(O)C(NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C(C)O)C(=O)O)O

IUPAC InChI

InChI=1S/C12H19N2O8P/c1-6-11(16)9(4-14-10(7(2)15)12(17)18)8(3-13-6)5-22-23(19,20)21/h3,7,10,14-16H,4-5H2,1-2H3,(H,17,18)(H2,19,20,21)

IUPAC InChI key

IZWQBQLGLAKRMN-UHFFFAOYSA-N
TLP

wwPDB Information

Atom count

42 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-07-17

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



TLP : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -1.735 0.231 0.415
2 C1 C C1 N N N 0 -2.512 1.369 -0.095
3 C2 C C2 N N N 0 -2.577 2.462 0.973
4 O1 O O1 N N N 0 -3.414 3.526 0.515
5 C3 C C3 N N N 0 -1.169 2.999 1.24
6 C4 C C4 N N N 0 -3.907 0.913 -0.434
7 O2 O O2 N N N 0 -4.8 1.789 -0.92
8 O3 O O3 N N N 0 -4.223 -0.241 -0.267
9 N2 N N2 N Y N 0 1.338 -3.625 0.534
10 C5 C C5 N Y N 0 0.058 -3.867 0.326
11 C6 C C6 N N N 0 -0.483 -5.256 0.55
12 C7 C C7 N Y N 0 -0.794 -2.858 -0.095
13 O4 O O4 N N N 0 -2.112 -3.112 -0.309
14 C8 C C8 N Y N 0 -0.281 -1.58 -0.298
15 C9 C C9 N N N 0 -1.171 -0.454 -0.756
16 C10 C C10 N Y N 0 1.07 -1.371 -0.073
17 C11 C C11 N Y N 0 1.856 -2.426 0.352
18 C12 C C12 N N N 0 1.674 -0.005 -0.278
19 O5 O O5 N N N 0 3.069 -0.05 0.03
20 P1 P P1 N N N 0 3.646 1.433 -0.209
21 O6 O O6 N N N 0 2.976 2.447 0.847
22 O7 O O7 N N N 0 5.244 1.427 -0.007
23 O8 O O8 N N N 0 3.326 1.872 -1.586
24 H1 H H1 N N N 0 -0.956 0.618 0.927
25 H2 H H2 N N N 0 -2.032 1.764 -0.991
26 H3 H H3 N N N 0 -2.988 2.047 1.893
27 H4 H H4 N N N 0 -3.016 3.865 -0.298
28 H5 H H5 N N N 0 -1.228 3.85 1.919
29 H6 H H6 N N N 0 -0.561 2.215 1.691
30 H7 H H7 N N N 0 -0.717 3.315 0.3
31 H8 H H8 N N N 0 -5.696 1.496 -1.137
32 H9 H H9 N N N 0 -1.528 -5.193 0.856
33 H10 H H10 N N N 0 -0.41 -5.827 -0.376
34 H11 H H11 N N N 0 0.095 -5.751 1.329
35 H12 H H12 N N N 0 -2.199 -3.378 -1.234
36 H13 H H13 N N N 0 -1.98 -0.855 -1.366
37 H14 H H14 N N N 0 -0.588 0.254 -1.345
38 H15 H H15 N N N 0 2.909 -2.268 0.532
39 H16 H H16 N N N 0 1.541 0.299 -1.316
40 H17 H H17 N N N 0 1.181 0.712 0.378
41 H18 H H18 N N N 0 3.209 2.126 1.729
42 H19 H H19 N N N 0 5.548 2.332 -0.158



TLP : Chemical Bonds

Total Number of Bonds: 42
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C1 N C sing 1.47 N N
2 N1 C9 N C sing 1.47 N N
3 N1 H1 N H sing 1.01 N N
4 C1 C2 C C sing 1.53 N N
5 C1 C4 C C sing 1.51 N N
6 C1 H2 C H sing 1.09 N N
7 C2 O1 C O sing 1.43 N N
8 C2 C3 C C sing 1.53 N N
9 C2 H3 C H sing 1.09 N N
10 O1 H4 O H sing 0.97 N N
11 C3 H5 C H sing 1.09 N N
12 C3 H6 C H sing 1.09 N N
13 C3 H7 C H sing 1.09 N N
14 C4 O2 C O sing 1.34 N N
15 C4 O3 C O doub 1.21 N N
16 O2 H8 O H sing 0.97 N N
17 N2 C5 N C doub 1.32 N Y
18 N2 C11 N C sing 1.32 N Y
19 C5 C6 C C sing 1.51 N N
20 C5 C7 C C sing 1.39 N Y
21 C6 H9 C H sing 1.09 N N
22 C6 H10 C H sing 1.09 N N
23 C6 H11 C H sing 1.09 N N
24 C7 O4 C O sing 1.36 N N
25 C7 C8 C C doub 1.39 N Y
26 O4 H12 O H sing 0.97 N N
27 C8 C9 C C sing 1.51 N N
28 C8 C10 C C sing 1.39 N Y
29 C9 H13 C H sing 1.09 N N
30 C9 H14 C H sing 1.09 N N
31 C10 C11 C C doub 1.38 N Y
32 C10 C12 C C sing 1.51 N N
33 C11 H15 C H sing 1.08 N N
34 C12 O5 C O sing 1.43 N N
35 C12 H16 C H sing 1.09 N N
36 C12 H17 C H sing 1.09 N N
37 O5 P1 O P sing 1.61 N N
38 P1 O6 P O sing 1.61 N N
39 P1 O7 P O sing 1.61 N N
40 P1 O8 P O doub 1.48 N N
41 O6 H18 O H sing 0.97 N N
42 O7 H19 O H sing 0.97 N N



TLP : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TLP 1lw4 Open in New Window Bound ligand 3 1