糖のPDB identification codeのリスト
List of PDB identification codes for sugars

2022.12.1 S. Fushinobu

PDB formatもアップデートされていて、いわゆる3-letter codeも近いうちに枯渇するそうですが、いちいち調べるのが面倒なので、主要なものだけメモしておきました。

Symbol	Name	Synonyms	ID
	alpha-D-glucopyranose	α-Glc; alpha-D-glucose	GLC
	beta-D-glucopyranose	β-Glc; beta-D-glucose	BGC
	alpha-D-mannopyranose	α-Man; alpha-D-mannose	MAN
	beta-D-mannopyranose	β-Man; beta-D-mannose	BMA
	alpha-D-galactopyranose	α-Gal; alpha-D-galactose	GLA
	beta-D-galactopyranose	β-Gal; beta-D-galactose	GAL
	2-acetamido-2-deoxy-alpha-D-glucopyranose	α-GlcNAc; N-acetyl-alpha-D-glucosamine	NDG
	2-acetamido-2-deoxy-beta-D-glucopyranose	β-GlcNAc; N-acetyl-beta-D-glucosamine	NAG
	2-acetamido-2-deoxy-alpha-D-galactopyranose	α-GalNAc; N-acetyl-alpha-D-galactosamine	A2G
	2-acetamido-2-deoxy-beta-D-glactopyranose	β-GalNAc; N-acetyl-beta-D-galactosamine	NGA
	alpha-L-rhamnopyranose	α-L-Rha; alpha-L-rhamnose	RAM
	beta-L-rhamnopyranose	β-L-Rha; beta-L-rhamnose	RM4
	alpha-L-fucopyranose	α-L-Fuc; alpha-L-fucose	FUC
	beta-L-fucopyranose	β-L-Fuc; beta-L-fucose	FUL
	alpha-L-arabinofuranose	α-L-Ara; alpha-L-arabinose	AHR
	alpha-d-xylopyranose	α-Xyl; alpha-D-xylose	XYS
	beta-d-xylopyranose	β-Xyl; beta-D-xylose	XYP
	n-acetyl-alpha-neuraminic acid	α-Neu5Ac; N-acetylneuraminic acid; sialic acid	SIA
	beta-D-fructofuranose	β-Fru; beta-D-fructose	FRU
	N-acetyl-beta-muramic acid	β-MurNAc; N-acetyl-muramic acid	AMU

D/L体やα/β、pyranose/furanoseの違いは、Nameの一部を書き換えてLigand Expoで探せば出てきます。
ここにない糖はSNFGのシンボルからリンクが貼ってあるPubChemのページで得たSMILESでLigand Expoをサーチすれば探せます。PubChemにPDB chemical IDの記載があれば、このページの存在意義は不要になるのですが。
間違いがあったら、asfushi@mail.ecc.u-tokyo.ac.jpまでお知らせください

For sugars with different D/L, alpha/beta, or pyranose/furanose, you can find them by rewriting part of the Name and searching for them in Ligand Expo. If the sugar you are looking for is not here, you can find it by searching Ligand Expo with SMILES obtained from the PubChem page linked from the SNFG symbol.