Chemical Components in the PDB

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PPD : Summary

Code

PPD

One-letter code

X

Molecule name

2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID

Synonyms

PYRIDOXYL-ASPARTIC ACID-5-MONOPHOSPHATE

Systematic names

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

Formula

C12 H17 N2 O9 P

Formal charge

0

Molecular weight

364.245 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)CC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O
SMILES CACTVS 3.341 Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CC(O)=O)C(O)=O)c1O
SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CC(=O)O)C(=O)O)O
Canonical SMILES CACTVS 3.341 Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CC(O)=O)C(O)=O)c1O
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CC(=O)O)C(=O)O)O

IUPAC InChI

InChI=1S/C12H17N2O9P/c1-6-11(17)8(4-14-9(12(18)19)2-10(15)16)7(3-13-6)5-23-24(20,21)22/h3,9,14,17H,2,4-5H2,1H3,(H,15,16)(H,18,19)(H2,20,21,22)/t9-/m0/s1

IUPAC InChI key

UKHLSCZNRCHWTM-VIFPVBQESA-N
PPD

wwPDB Information

Atom count

41 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



PPD : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 3.866 0.664 0.325
2 C2 C C2 N Y N 0 3.811 0.436 -0.971
3 C2A C C2A N N N 0 5.015 0.723 -1.831
4 C3 C C3 N Y N 0 2.654 -0.058 -1.554
5 O3 O O3 N N N 0 2.601 -0.291 -2.892
6 C4 C C4 N Y N 0 1.551 -0.324 -0.748
7 C4A C C4A N N N 0 0.276 -0.868 -1.338
8 C5 C C5 N Y N 0 1.653 -0.07 0.609
9 C6 C C6 N Y N 0 2.838 0.429 1.116
10 C5A C C5A N N N 0 0.485 -0.335 1.524
11 O4P O O4P N N N 0 0.842 0.005 2.865
12 P P P N N N 0 -0.444 -0.3 3.782
13 O1P O O1P N N N 0 -0.792 -1.735 3.68
14 O2P O O2P N N N 0 -0.11 0.063 5.314
15 O3P O O3P N N N 0 -1.687 0.589 3.277
16 N N N N N N 0 -0.593 0.245 -1.737
17 CA C CA S N N 0 -1.811 -0.351 -2.301
18 CB C CB N N N 0 -2.998 0.581 -2.053
19 CG C CG N N N 0 -3.177 0.782 -0.57
20 OD1 O OD1 N N N 0 -2.432 0.235 0.207
21 OD2 O OD2 N N N 0 -4.165 1.568 -0.113
22 C C C N N N 0 -1.632 -0.551 -3.784
23 O O O N N N 0 -2.202 -1.457 -4.344
24 OXT O OXT N N N 0 -0.839 0.276 -4.482
25 H2A1 H 1H2A N N N 0 5.643 -0.165 -1.885
26 H2A2 H 2H2A N N N 0 4.688 0.998 -2.834
27 H2A3 H 3H2A N N N 0 5.584 1.545 -1.397
28 HO3 H HO3 N N N 0 2.282 0.523 -3.305
29 H4A1 H 1H4A N N N 0 0.511 -1.477 -2.212
30 H4A2 H 2H4A N N N 0 -0.234 -1.481 -0.596
31 H6 H H6 N N N 0 2.923 0.628 2.174
32 H5A1 H 1H5A N N N 0 -0.366 0.267 1.21
33 H5A2 H 2H5A N N N 0 0.219 -1.391 1.477
34 HOP2 H 2HOP N N N 0 -0.905 -0.134 5.828
35 HOP3 H 3HOP N N N 0 -1.419 1.515 3.36
36 HN H HN N N N 0 -0.867 0.717 -0.888
37 HA H HA N N N 0 -1.999 -1.313 -1.825
38 HB1 H 1HB N N N 0 -2.81 1.543 -2.529
39 HB2 H 2HB N N N 0 -3.902 0.139 -2.471
40 HOD H HOD N N N 0 -4.28 1.697 0.837
41 HXT H HXT N N N 0 -0.724 0.147 -5.434



PPD : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.32 N Y
2 N1 C6 N C sing 1.32 N Y
3 C2 C2A C C sing 1.51 N N
4 C2 C3 C C sing 1.39 N Y
5 C2A H2A1 C H sing 1.09 N N
6 C2A H2A2 C H sing 1.09 N N
7 C2A H2A3 C H sing 1.09 N N
8 C3 O3 C O sing 1.36 N N
9 C3 C4 C C doub 1.39 N Y
10 O3 HO3 O H sing 0.97 N N
11 C4 C4A C C sing 1.51 N N
12 C4 C5 C C sing 1.38 N Y
13 C4A N C N sing 1.47 N N
14 C4A H4A1 C H sing 1.09 N N
15 C4A H4A2 C H sing 1.09 N N
16 C5 C6 C C doub 1.38 N Y
17 C5 C5A C C sing 1.51 N N
18 C6 H6 C H sing 1.08 N N
19 C5A O4P C O sing 1.43 N N
20 C5A H5A1 C H sing 1.09 N N
21 C5A H5A2 C H sing 1.09 N N
22 O4P P O P sing 1.61 N N
23 P O1P P O doub 1.48 N N
24 P O2P P O sing 1.61 N N
25 P O3P P O sing 1.61 N N
26 O2P HOP2 O H sing 0.97 N N
27 O3P HOP3 O H sing 0.97 N N
28 N CA N C sing 1.47 N N
29 N HN N H sing 1.01 N N
30 CA CB C C sing 1.53 N N
31 CA C C C sing 1.51 N N
32 CA HA C H sing 1.09 N N
33 CB CG C C sing 1.51 N N
34 CB HB1 C H sing 1.09 N N
35 CB HB2 C H sing 1.09 N N
36 CG OD1 C O doub 1.21 N N
37 CG OD2 C O sing 1.34 N N
38 OD2 HOD O H sing 0.97 N N
39 C O C O doub 1.21 N N
40 C OXT C O sing 1.34 N N
41 OXT HXT O H sing 0.97 N N



PPD : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
PPD 1akb Open in New Window Bound ligand 1 1
PPD 1arg Open in New Window Bound ligand 2 1
PPD 1arh Open in New Window Bound ligand 2 1