Chemical Components in the PDB

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  • 0MK (Stereoisomer)
  • ARA (Stereoisomer)
  • ARB (Stereoisomer)
  • HSY (Stereoisomer)
  • LXC (Stereoisomer)
  • LDY (Stereoisomer)
  • RIP (Stereoisomer)
  • XYP (Stereoisomer)

XYS : Summary

Code

XYS

One-letter code

X

Molecule name

XYLOPYRANOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 alpha-D-xylopyranose
OpenEye OEToolkits 1.5.0 (2S,3R,4S,5R)-oxane-2,3,4,5-tetrol

Formula

C5 H10 O5

Formal charge

0

Molecular weight

150.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(O)COC(O)C1O
SMILES CACTVS 3.341 O[CH]1CO[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(O1)O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1CO[C@H](O)[C@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O

IUPAC InChI

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5+/m1/s1

IUPAC InChI key

SRBFZHDQGSBBOR-LECHCGJUSA-N
XYS

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



XYS : Atoms of Molecule

Total Number of Atoms: 20
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 -0.639 0.258 -1.454
2 C2 C C2 R N N 0 0.752 0.486 -0.86
3 C3 C C3 S N N 0 0.832 -0.202 0.506
4 C4 C C4 R N N 0 -0.335 0.286 1.37
5 C5 C C5 N N N 0 -1.645 0.073 0.608
6 H1 H H1 N N N 0 -0.695 0.726 -2.437
7 H2 H H2 N N N 0 0.927 1.555 -0.74
8 H3 H H3 N N N 0 0.763 -1.282 0.377
9 H4 H H4 N N N 0 -0.208 1.346 1.589
10 H51 H 1H5 N N N 0 -1.759 -0.984 0.371
11 H52 H 2H5 N N N 0 -2.481 0.397 1.227
12 HO1 H HO1 N N N 0 -1.759 -1.246 -1.963
13 HO2 H HO2 N N N 0 1.65 0.393 -2.581
14 HO3 H HO3 N N N 0 2.08 -0.326 1.991
15 HO4 H HO4 N N N 0 -1.117 -0.117 3.103
16 O1 O O1 N N Y 0 -0.876 -1.145 -1.582
17 O2 O O2 N N N 0 1.74 -0.064 -1.734
18 O3 O O3 N N N 0 2.072 0.126 1.136
19 O4 O O4 N N N 0 -0.368 -0.453 2.592
20 O5 O O5 N N N 0 -1.628 0.83 -0.6



XYS : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 O2 C O sing 1.43 N N
7 C2 H2 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 O3 C O sing 1.43 N N
10 C3 H3 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 C5 O5 C O sing 1.43 N N
15 C5 H51 C H sing 1.09 N N
16 C5 H52 C H sing 1.09 N N
17 O1 HO1 O H sing 0.97 N N
18 O2 HO2 O H sing 0.97 N N
19 O3 HO3 O H sing 0.97 N N
20 O4 HO4 O H sing 0.97 N N



XYS : Used in PDB Entries

Total Number of PDB Entries: 66
Ligand Code PDB Entry ID Type Total Distinct
XYS 1apv Open in New Window Bound ligand 1 1
XYS 1b3v Open in New Window Bound ligand 1 1
XYS 1b3w Open in New Window Bound ligand 1 1
XYS 1b3y Open in New Window Bound ligand 1 1
XYS 1b3z Open in New Window Bound ligand 1 1
XYS 1cpo Open in New Window Bound ligand 2 2
XYS 1f8q Open in New Window Bound ligand 1 1
XYS 1gor Open in New Window Bound ligand 1 1
XYS 1h12 Open in New Window Bound ligand 1 1
XYS 1h4h Open in New Window Bound ligand 4 1
XYS 1j10 Open in New Window Bound ligand 1 1
XYS 1mn0 Open in New Window Bound ligand 2 1
XYS 1ppl Open in New Window Bound ligand 1 1
XYS 1qk0 Open in New Window Bound ligand 1 1
XYS 1umz Open in New Window Bound ligand 4 2
XYS 1uqy Open in New Window Bound ligand 1 1
XYS 1uqz Open in New Window Bound ligand 1 1
XYS 1ur1 Open in New Window Bound ligand 1 1
XYS 1ur2 Open in New Window Bound ligand 1 1
XYS 1v6u Open in New Window Bound ligand 1 1
XYS 1vbr Open in New Window Bound ligand 2 1
XYS 1w9t Open in New Window Bound ligand 2 1
XYS 2bfg Open in New Window Bound ligand 8 2
XYS 2bs6 Open in New Window Bound ligand 3 1
XYS 2c8n Open in New Window Bound ligand 6 1
XYS 2cdc Open in New Window Bound ligand 6 1
XYS 2cn3 Open in New Window Bound ligand 12 6
XYS 2cnc Open in New Window Bound ligand 1 1
XYS 2d20 Open in New Window Bound ligand 4 2
XYS 2d22 Open in New Window Bound ligand 4 2
XYS 2d23 Open in New Window Bound ligand 4 2
XYS 2d24 Open in New Window Bound ligand 18 11
XYS 2d44 Open in New Window Bound ligand 4 2
XYS 2dua Open in New Window Bound ligand 1 1
XYS 2ebs Open in New Window Bound ligand 6 3
XYS 2exj Open in New Window Bound ligand 8 2
XYS 2exk Open in New Window Bound ligand 8 2
XYS 2fgl Open in New Window Bound ligand 8 5
XYS 2fuq Open in New Window Bound ligand 2 1
XYS 2g3j Open in New Window Bound ligand 4 2
XYS 2hcz Open in New Window Bound ligand 1 1
XYS 2hjp Open in New Window Bound ligand 1 1
XYS 2jen Open in New Window Bound ligand 4 4
XYS 2jeq Open in New Window Bound ligand 2 2
XYS 2vh9 Open in New Window Bound ligand 6 2
XYS 2vlc Open in New Window Bound ligand 1 1
XYS 2xsp Open in New Window Bound ligand 1 1
XYS 2yfz Open in New Window Bound ligand 1 1
XYS 2yih Open in New Window Bound ligand 1 1
XYS 2ypj Open in New Window Bound ligand 3 3
XYS 3e80 Open in New Window Bound ligand 3 1
XYS 3rdk Open in New Window Bound ligand 2 1
XYS 3ugh Open in New Window Bound ligand 1 1
XYS 3vl9 Open in New Window Bound ligand 3 3
XYS 3vsv Open in New Window Bound ligand 9 1
XYS 3w27 Open in New Window Bound ligand 1 1
XYS 3w28 Open in New Window Bound ligand 1 1
XYS 3w29 Open in New Window Bound ligand 1 1
XYS 3xis Open in New Window Bound ligand 1 1
XYS 3zmr Open in New Window Bound ligand 6 6
XYS 4bj0 Open in New Window Bound ligand 3 3
XYS 4cuo Open in New Window Bound ligand 1 1
XYS 4fe7 Open in New Window Bound ligand 1 1
XYS 4g68 Open in New Window Bound ligand 2 1
XYS 4hkw Open in New Window Bound ligand 1 1
XYS 4xis Open in New Window Bound ligand 1 1