Chemical Components in the PDB

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PMM : Summary

Code

PMM

One-letter code

X

Molecule name

PTERIN-6-YL-METHYL-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl dihydrogen phosphate
OpenEye OEToolkits 1.5.0 (2-amino-4-oxo-3H-pteridin-6-yl)methyl dihydrogen phosphate

Formula

C7 H8 N5 O5 P

Formal charge

0

Molecular weight

273.143 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCc1nc2C(=O)NC(=Nc2nc1)N
SMILES CACTVS 3.341 NC1=Nc2ncc(CO[P](O)(O)=O)nc2C(=O)N1
SMILES OpenEye OEToolkits 1.5.0 c1c(nc2c(n1)N=C(NC2=O)N)COP(=O)(O)O
Canonical SMILES CACTVS 3.341 NC1=Nc2ncc(CO[P](O)(O)=O)nc2C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.5.0 c1c(nc2c(n1)N=C(NC2=O)N)COP(=O)(O)O

IUPAC InChI

InChI=1S/C7H8N5O5P/c8-7-11-5-4(6(13)12-7)10-3(1-9-5)2-17-18(14,15)16/h1H,2H2,(H2,14,15,16)(H3,8,9,11,12,13)

IUPAC InChI key

AJXFJEHKGGCFNM-UHFFFAOYSA-N
PMM

wwPDB Information

Atom count

26 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2000-05-12

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PMM : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N5 N N5 N Y N 0 -0.892 0.022 0.72
2 C6 C C6 N Y N 0 -0.025 0.015 -0.272
3 C7 C C7 N Y N 0 1.342 -0.004 -0.016
4 N8 N N8 N Y N 0 1.795 -0.016 1.221
5 N1 N N1 N Y N 0 1.355 -0.02 3.517
6 C2 C C2 N Y N 0 0.513 -0.013 4.521
7 N2 N N2 N N N 0 1.017 -0.025 5.796
8 N3 N N3 N Y N 0 -0.839 0.0 4.358
9 C4 C C4 N Y N 0 -1.38 0.016 3.118
10 O4 O O4 N N N 0 -2.586 0.032 2.954
11 C4A C C4A N Y N 0 -0.454 0.01 1.972
12 C8A C C8A N Y N 0 0.933 -0.009 2.239
13 C9 C C9 N N N 0 -0.519 0.029 -1.695
14 O10 O O10 N N N 0 0.597 0.018 -2.587
15 PA P PA N N N 0 0.0 0.034 -4.082
16 O1P O O1P N N N 0 -0.815 1.254 -4.275
17 O2P O O2P N N N 0 1.209 0.022 -5.144
18 O3P O O3P N N N 0 -0.922 -1.267 -4.305
19 H7 H H7 N N N 0 2.04 -0.009 -0.84
20 HN21 H 1HN2 N N N 0 1.977 -0.039 5.938
21 HN22 H 2HN2 N N N 0 0.415 -0.016 6.556
22 HN3 H HN3 N N N 0 -1.419 0.002 5.136
23 H91 H 1H9 N N N 0 -1.135 -0.851 -1.875
24 H92 H 2H9 N N N 0 -1.111 0.928 -1.866
25 HOP2 H 2HOP N N N 0 0.808 0.032 -6.024
26 HOP3 H 3HOP N N N 0 -0.354 -2.038 -4.17



PMM : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N5 C6 N C doub 1.32 N Y
2 N5 C4A N C sing 1.33 N Y
3 C6 C7 C C sing 1.39 N Y
4 C6 C9 C C sing 1.51 N N
5 C7 N8 C N doub 1.32 N Y
6 C7 H7 C H sing 1.08 N N
7 N8 C8A N C sing 1.33 N Y
8 N1 C2 N C doub 1.31 N Y
9 N1 C8A N C sing 1.35 N Y
10 C2 N2 C N sing 1.37 N N
11 C2 N3 C N sing 1.36 N Y
12 N2 HN21 N H sing 0.97 N N
13 N2 HN22 N H sing 0.97 N N
14 N3 C4 N C sing 1.35 N Y
15 N3 HN3 N H sing 0.97 N N
16 C4 O4 C O doub 1.22 N N
17 C4 C4A C C sing 1.47 N Y
18 C4A C8A C C doub 1.41 N Y
19 C9 O10 C O sing 1.43 N N
20 C9 H91 C H sing 1.09 N N
21 C9 H92 C H sing 1.09 N N
22 O10 PA O P sing 1.61 N N
23 PA O1P P O doub 1.48 N N
24 PA O2P P O sing 1.61 N N
25 PA 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



PMM : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
PMM 1eye Open in New Window Bound ligand 1 1
PMM 1twz Open in New Window Bound ligand 2 1
PMM 2bmb Open in New Window Bound ligand 2 1
PMM 2veg Open in New Window Bound ligand 1 1
PMM 6omz Open in New Window Bound ligand 1 1
PMM 6ucz Open in New Window Bound ligand 2 1