Chemical Components in the PDB

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

XYP : Summary

Code

XYP

One-letter code

X

Molecule name

BETA-D-XYLOPYRANOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 beta-D-xylopyranose
OpenEye OEToolkits 1.5.0 (2R,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-KKQCNMDGSA-N
XYP

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

D-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



XYP : 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 O4A O O4A N N Y 0 0.501 -0.13 -2.746
2 C1B C C1B R N N 0 0.509 0.253 -1.37
3 C2B C C2B R N N 0 -0.78 -0.228 -0.701
4 C3B C C3B S N N 0 -0.779 0.213 0.766
5 C4B C C4B R N N 0 0.519 -0.269 1.423
6 C5B C C5B N N N 0 1.71 0.215 0.593
7 O2B O O2B N N N 0 -1.907 0.337 -1.372
8 O3B O O3B N N N 0 -1.904 -0.354 1.439
9 O4B O O4B N N N 0 0.611 0.26 2.747
10 O5B O O5B N N N 0 1.637 -0.331 -0.721
11 HO4A H HO4A N N N 0 1.325 0.194 -3.132
12 H1B H H1B N N N 0 0.571 1.338 -1.297
13 H2B H H2B N N N 0 -0.833 -1.316 -0.752
14 H3B H H3B N N N 0 -0.831 1.301 0.82
15 H4B H H4B N N N 0 0.523 -1.358 1.465
16 H5B1 H 1H5B N N N 0 1.692 1.303 0.535
17 H5B2 H 2H5B N N N 0 2.637 -0.105 1.068
18 HO2B H HO2B N N N 0 -1.865 0.037 -2.291
19 HO3B H HO3B N N N 0 -1.864 -0.051 2.356
20 HO4B H HO4B N N N 0 1.441 -0.064 3.121



XYP : 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 O4A C1B O C sing 1.43 N N
2 O4A HO4A O H sing 0.97 N N
3 C1B C2B C C sing 1.53 N N
4 C1B O5B C O sing 1.43 N N
5 C1B H1B C H sing 1.09 N N
6 C2B C3B C C sing 1.53 N N
7 C2B O2B C O sing 1.43 N N
8 C2B H2B C H sing 1.09 N N
9 C3B C4B C C sing 1.53 N N
10 C3B O3B C O sing 1.43 N N
11 C3B H3B C H sing 1.09 N N
12 C4B C5B C C sing 1.53 N N
13 C4B O4B C O sing 1.43 N N
14 C4B H4B C H sing 1.09 N N
15 C5B O5B C O sing 1.42 N N
16 C5B H5B1 C H sing 1.09 N N
17 C5B H5B2 C H sing 1.09 N N
18 O2B HO2B O H sing 0.97 N N
19 O3B HO3B O H sing 0.97 N N
20 O4B HO4B O H sing 0.97 N N



XYP : Used in PDB Entries

Total Number of PDB Entries: 169
Ligand Code PDB Entry ID Type Total Distinct
XYP 1ax0 Open in New Window Bound ligand 1 1
XYP 1ax1 Open in New Window Bound ligand 1 1
XYP 1ax2 Open in New Window Bound ligand 1 1
XYP 1axy Open in New Window Bound ligand 1 1
XYP 1axz Open in New Window Bound ligand 1 1
XYP 1b30 Open in New Window Bound ligand 3 3
XYP 1b3v Open in New Window Bound ligand 3 1
XYP 1b3w Open in New Window Bound ligand 2 2
XYP 1b3x Open in New Window Bound ligand 4 4
XYP 1b3y Open in New Window Bound ligand 3 3
XYP 1b3z Open in New Window Bound ligand 5 5
XYP 1bcx Open in New Window Bound ligand 2 2
XYP 1bvv Open in New Window Bound ligand 1 1
XYP 1c5i Open in New Window Bound ligand 1 1
XYP 1cb8 Open in New Window Bound ligand 1 1
XYP 1cf5 Open in New Window Bound ligand 2 1
XYP 1dbg Open in New Window Bound ligand 1 1
XYP 1dbo Open in New Window Bound ligand 1 1
XYP 1dwa Open in New Window Bound ligand 2 2
XYP 1dwf Open in New Window Bound ligand 2 2
XYP 1dwg Open in New Window Bound ligand 2 2
XYP 1dwh Open in New Window Bound ligand 2 2
XYP 1dwi Open in New Window Bound ligand 2 2
XYP 1dwj Open in New Window Bound ligand 2 2
XYP 1e0x Open in New Window Bound ligand 2 1
XYP 1e4m Open in New Window Bound ligand 2 2
XYP 1e5n Open in New Window Bound ligand 10 5
XYP 1e6q Open in New Window Bound ligand 2 2
XYP 1e6s Open in New Window Bound ligand 2 2
XYP 1e6x Open in New Window Bound ligand 2 2
XYP 1e70 Open in New Window Bound ligand 2 2
XYP 1e71 Open in New Window Bound ligand 2 2
XYP 1e72 Open in New Window Bound ligand 2 2
XYP 1e73 Open in New Window Bound ligand 2 2
XYP 1fh7 Open in New Window Bound ligand 1 1
XYP 1fh8 Open in New Window Bound ligand 1 1
XYP 1fh9 Open in New Window Bound ligand 1 1
XYP 1fhd Open in New Window Bound ligand 1 1
XYP 1gny Open in New Window Bound ligand 5 5
XYP 1goq Open in New Window Bound ligand 6 3
XYP 1gor Open in New Window Bound ligand 1 1
XYP 1gqj Open in New Window Bound ligand 4 2
XYP 1gql Open in New Window Bound ligand 4 2
XYP 1h12 Open in New Window Bound ligand 1 1
XYP 1h4h Open in New Window Bound ligand 8 2
XYP 1hm2 Open in New Window Bound ligand 1 1
XYP 1hm3 Open in New Window Bound ligand 1 1
XYP 1hmu Open in New Window Bound ligand 1 1
XYP 1hmw Open in New Window Bound ligand 1 1
XYP 1ioo Open in New Window Bound ligand 2 2
XYP 1iqq Open in New Window Bound ligand 1 1
XYP 1isv Open in New Window Bound ligand 6 1
XYP 1isw Open in New Window Bound ligand 14 3
XYP 1isx Open in New Window Bound ligand 17 6
XYP 1j10 Open in New Window Bound ligand 7 1
XYP 1k9f Open in New Window Bound ligand 2 2
XYP 1l8n Open in New Window Bound ligand 2 2
XYP 1mc9 Open in New Window Bound ligand 5 5
XYP 1myr Open in New Window Bound ligand 2 2
XYP 1nae Open in New Window Bound ligand 3 3
XYP 1od8 Open in New Window Bound ligand 2 1
XYP 1ofl Open in New Window Bound ligand 1 1
XYP 1ofm Open in New Window Bound ligand 1 1
XYP 1px8 Open in New Window Bound ligand 2 1
XYP 1qh7 Open in New Window Bound ligand 2 1
XYP 1qk0 Open in New Window Bound ligand 1 1
XYP 1r87 Open in New Window Bound ligand 5 5
XYP 1uqy Open in New Window Bound ligand 6 6
XYP 1uqz Open in New Window Bound ligand 5 5
XYP 1ur1 Open in New Window Bound ligand 1 1
XYP 1ur2 Open in New Window Bound ligand 5 5
XYP 1us2 Open in New Window Bound ligand 8 4
XYP 1ux7 Open in New Window Bound ligand 3 3
XYP 1uxx Open in New Window Bound ligand 5 5
XYP 1uy2 Open in New Window Bound ligand 2 2
XYP 1uy3 Open in New Window Bound ligand 3 3
XYP 1uy4 Open in New Window Bound ligand 4 4
XYP 1uyz Open in New Window Bound ligand 4 4
XYP 1uzy Open in New Window Bound ligand 1 1
XYP 1v0k Open in New Window Bound ligand 1 1
XYP 1v0l Open in New Window Bound ligand 1 1
XYP 1v0m Open in New Window Bound ligand 1 1
XYP 1v0n Open in New Window Bound ligand 1 1
XYP 1v6u Open in New Window Bound ligand 14 5
XYP 1v6v Open in New Window Bound ligand 19 9
XYP 1v6w Open in New Window Bound ligand 8 5
XYP 1v6x Open in New Window Bound ligand 18 9
XYP 1vbr Open in New Window Bound ligand 2 1
XYP 1w9b Open in New Window Bound ligand 2 2
XYP 1w9d Open in New Window Bound ligand 2 2
XYP 1w9t Open in New Window Bound ligand 8 3
XYP 1wu5 Open in New Window Bound ligand 1 1
XYP 1wu6 Open in New Window Bound ligand 2 2
XYP 1x38 Open in New Window Bound ligand 2 2
XYP 1x39 Open in New Window Bound ligand 2 2
XYP 1xwq Open in New Window Bound ligand 3 3
XYP 2b46 Open in New Window Bound ligand 2 2
XYP 2b4f Open in New Window Bound ligand 10 5
XYP 2bfg Open in New Window Bound ligand 2 1
XYP 2bnj Open in New Window Bound ligand 2 2
XYP 2cdc Open in New Window Bound ligand 4 1
XYP 2cnc Open in New Window Bound ligand 1 1
XYP 2e2q Open in New Window Bound ligand 1 1
XYP 2hox Open in New Window Bound ligand 1 1
XYP 2nqy Open in New Window Bound ligand 2 1
XYP 2qz2 Open in New Window Bound ligand 6 3
XYP 2qz3 Open in New Window Bound ligand 12 3
XYP 2v4v Open in New Window Bound ligand 1 1
XYP 2vgd Open in New Window Bound ligand 5 5
XYP 2vlc Open in New Window Bound ligand 1 1
XYP 2vrq Open in New Window Bound ligand 8 5
XYP 2w5f Open in New Window Bound ligand 6 6
XYP 2wxd Open in New Window Bound ligand 2 2
XYP 2wys Open in New Window Bound ligand 6 3
XYP 2wze Open in New Window Bound ligand 6 6
XYP 2xyl Open in New Window Bound ligand 1 1
XYP 2y24 Open in New Window Bound ligand 3 3
XYP 2y64 Open in New Window Bound ligand 5 5
XYP 2y6k Open in New Window Bound ligand 4 4
XYP 2y6l Open in New Window Bound ligand 5 5
XYP 3bwh Open in New Window Bound ligand 1 1
XYP 3c6q Open in New Window Bound ligand 2 1
XYP 3c7f Open in New Window Bound ligand 3 3
XYP 3c7g Open in New Window Bound ligand 4 1
XYP 3c7h Open in New Window Bound ligand 3 3
XYP 3ca0 Open in New Window Bound ligand 1 1
XYP 3fyt Open in New Window Bound ligand 6 1
XYP 3fyu Open in New Window Bound ligand 7 1
XYP 3kl5 Open in New Window Bound ligand 8 2
XYP 3m9x Open in New Window Bound ligand 1 1
XYP 3ma0 Open in New Window Bound ligand 3 1
XYP 3mmd Open in New Window Bound ligand 5 5
XYP 3msd Open in New Window Bound ligand 4 2
XYP 3msg Open in New Window Bound ligand 5 3
XYP 3mua Open in New Window Bound ligand 5 3
XYP 3mui Open in New Window Bound ligand 6 2
XYP 3nj3 Open in New Window Bound ligand 4 1
XYP 3rdk Open in New Window Bound ligand 4 2
XYP 3s5y Open in New Window Bound ligand 3 3
XYP 3s5z Open in New Window Bound ligand 2 2
XYP 3ug5 Open in New Window Bound ligand 15 1
XYP 3usu Open in New Window Bound ligand 1 1
XYP 3vpl Open in New Window Bound ligand 4 2
XYP 3vsv Open in New Window Bound ligand 26 1
XYP 3vzm Open in New Window Bound ligand 1 1
XYP 3vzn Open in New Window Bound ligand 2 1
XYP 3vzo Open in New Window Bound ligand 1 1
XYP 3w25 Open in New Window Bound ligand 2 2
XYP 3w26 Open in New Window Bound ligand 3 3
XYP 3w27 Open in New Window Bound ligand 1 1
XYP 3w28 Open in New Window Bound ligand 2 2
XYP 3w29 Open in New Window Bound ligand 3 3
XYP 3wn1 Open in New Window Bound ligand 3 3
XYP 3wn2 Open in New Window Bound ligand 5 5
XYP 3wp6 Open in New Window Bound ligand 3 3
XYP 3zkk Open in New Window Bound ligand 4 4
XYP 3zkl Open in New Window Bound ligand 3 3
XYP 3zxk Open in New Window Bound ligand 6 3
XYP 4a5g Open in New Window Bound ligand 3 3
XYP 4c1t Open in New Window Bound ligand 3 3
XYP 4c1u Open in New Window Bound ligand 2 2
XYP 4g68 Open in New Window Bound ligand 4 2
XYP 4gby Open in New Window Bound ligand 1 1
XYP 4hk8 Open in New Window Bound ligand 6 6
XYP 4hk9 Open in New Window Bound ligand 3 3
XYP 4hkw Open in New Window Bound ligand 4 4
XYP 4lw6 Open in New Window Bound ligand 2 2
XYP 4m4k Open in New Window Bound ligand 2 2
XYP 4o8p Open in New Window Bound ligand 4 4