Chemical Components in the PDB

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XMP : Summary

Code

XMP

One-letter code

X

Molecule name

XANTHOSINE-5'-MONOPHOSPHATE

Synonyms

5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-xanthylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2,6-dioxo-3H-purin-7-ium-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H14 N4 O9 P

Formal charge

1

Molecular weight

365.213 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C3Nc1c([nH+]cn1C2OC(C(O)C2O)COP(=O)(O)O)C(=O)N3
SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23
SMILES OpenEye OEToolkits 1.5.0 c1[nH+]c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)NC(=O)NC2=O
Canonical SMILES CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23
Canonical SMILES OpenEye OEToolkits 1.5.0 c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)NC(=O)NC2=O

IUPAC InChI

InChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/p+1/t3-,5-,6-,9-/m1/s1

IUPAC InChI key

DCTLYFZHFGENCW-UUOKFMHZSA-O
XMP

wwPDB Information

Atom count

38 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-12

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



XMP : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 5.08 0.916 0.179
2 O1P O O1P N N N 0 5.464 1.919 1.379
3 O2P O O2P N N N 0 6.254 -0.17 -0.0090
4 O5' O O5' N N N 0 3.702 0.162 0.531
5 O3P O O3P N N N 0 4.916 1.686 -1.074
6 C5' C C5' N N N 0 3.041 -0.718 -0.381
7 C4' C C4' R N N 0 1.766 -1.261 0.267
8 O4' O O4' N N N 0 0.824 -0.193 0.462
9 C1' C C1' R N N 0 -0.493 -0.754 0.278
10 N9 N N9 N Y N 0 -1.461 0.297 -0.045
11 C4 C C4 N Y N 0 -2.805 0.239 0.15
12 N3 N N3 N N N 0 -3.664 -0.707 0.662
13 N1 N N1 N N N 0 -5.532 0.682 0.309
14 C2 C C2 N N N 0 -4.986 -0.471 0.73
15 O2 O O2 N N N 0 -5.712 -1.332 1.188
16 C6 C C6 N N N 0 -4.764 1.666 -0.206
17 O6 O O6 N N N 0 -5.262 2.71 -0.587
18 C5 C C5 N Y N 0 -3.319 1.449 -0.298
19 N7 N N7 N Y N 1 -2.278 2.191 -0.746
20 C8 C C8 N Y N 0 -1.176 1.514 -0.592
21 C2' C C2' R N N 0 -0.311 -1.717 -0.923
22 O2' O O2' N N N 0 -1.295 -2.753 -0.9
23 C3' C C3' S N N 0 1.103 -2.292 -0.667
24 O3' O O3' N N N 0 1.016 -3.565 -0.024
25 HOP1 H HOP1 N N N 0 6.286 2.408 1.235
26 HOP2 H HOP2 N N N 0 6.417 -0.712 0.775
27 H5'2 H H5'2 N N N 0 2.784 -0.172 -1.289
28 H5'1 H H5'1 N N N 0 3.704 -1.546 -0.631
29 H4' H H4' N N N 0 2.006 -1.724 1.224
30 H1' H H1' N N N 0 -0.805 -1.301 1.168
31 H3 H H3 N N N 0 -3.311 -1.554 0.976
32 H1 H H1 N N N 0 -6.491 0.809 0.377
33 H7 H H7 N N N 0 -2.342 3.084 -1.118
34 H8 H H8 N N N 0 -0.189 1.862 -0.86
35 H2' H H2' N N N 0 -0.345 -1.172 -1.867
36 H2O1 H H2O1 N N N 0 -1.223 -3.381 -1.632
37 H3' H H3' N N N 0 1.657 -2.373 -1.602
38 H3O1 H H3O1 N N N 0 0.606 -4.253 -0.566



XMP : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O sing 1.61 N N
2 P O2P P O sing 1.61 N N
3 P O5' P O sing 1.61 N N
4 P O3P P O doub 1.48 N N
5 O1P HOP1 O H sing 0.97 N N
6 O2P HOP2 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5'2 C H sing 1.09 N N
10 C5' H5'1 C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C1' N9 C N sing 1.46 N N
16 C1' C2' C C sing 1.55 N N
17 C1' H1' C H sing 1.09 N N
18 N9 C4 N C sing 1.36 N Y
19 N9 C8 N C sing 1.36 N Y
20 C4 N3 C N sing 1.38 N N
21 C4 C5 C C doub 1.39 N Y
22 N3 C2 N C sing 1.34 N N
23 N3 H3 N H sing 0.97 N N
24 N1 C2 N C sing 1.34 N N
25 N1 C6 N C sing 1.35 N N
26 N1 H1 N H sing 0.97 N N
27 C2 O2 C O doub 1.22 N N
28 C6 O6 C O doub 1.22 N N
29 C6 C5 C C sing 1.46 N N
30 C5 N7 C N sing 1.35 N Y
31 N7 C8 N C doub 1.3 N Y
32 N7 H7 N H sing 0.97 N N
33 C8 H8 C H sing 1.08 N N
34 C2' O2' C O sing 1.43 N N
35 C2' C3' C C sing 1.55 N N
36 C2' H2' C H sing 1.09 N N
37 O2' H2O1 O H sing 0.97 N N
38 C3' O3' C O sing 1.43 N N
39 C3' H3' C H sing 1.09 N N
40 O3' H3O1 O H sing 0.97 N N



XMP : Used in PDB Entries

Total Number of PDB Entries: 23
Ligand Code PDB Entry ID Type Total Distinct
XMP 1lol Open in New Window Bound ligand 2 1
XMP 1m9n Open in New Window Bound ligand 2 1
XMP 1mei Open in New Window Bound ligand 1 1
XMP 1mew Open in New Window Bound ligand 1 1
XMP 1p4r Open in New Window Bound ligand 1 1
XMP 1pkx Open in New Window Bound ligand 2 1
XMP 1pl0 Open in New Window Bound ligand 2 1
XMP 1qk5 Open in New Window Bound ligand 2 1
XMP 2cu0 Open in New Window Bound ligand 2 1
XMP 2czf Open in New Window Bound ligand 2 1
XMP 2vxo Open in New Window Bound ligand 2 1
XMP 2ywc Open in New Window Bound ligand 4 1
XMP 3bpw Open in New Window Bound ligand 2 1
XMP 3bvj Open in New Window Bound ligand 2 1
XMP 3tsd Open in New Window Bound ligand 2 1
XMP 3uow Open in New Window Bound ligand 2 1
XMP 4qq3 Open in New Window Bound ligand 1 1
XMP 4x3z Open in New Window Bound ligand 2 1
XMP 4zqm Open in New Window Bound ligand 1 1
XMP 5upx Open in New Window Bound ligand 1 1
XMP 6jp9 Open in New Window Bound ligand 4 1
XMP 6mxb Open in New Window Bound ligand 6 1
XMP 6mxg Open in New Window Bound ligand 2 1