This library represents a list of names and abbreviations for molecules and non-standard protein residues collected over the past several years at BMRB. The nomenclature used, at this time, may not correspond to IUPAC rules and the synonyms or abbreviations provided as indented lists were, in most instances, developed at BMRB for use in storing the data in the relational database.
For many of these molecules, two-dimensional representations of their chemical structure and atom nomenclature tables have been constructed at BMRB. HTML links between the molecule names in the library and these data will be provided in the future.
Authors submitting data to BMRB can use the molecule names listed here in the non-polymer section of the BMRB electronic deposition form. If one of these names is used, the author will not need to fill out the required information needed to define the atoms and bonds in the molecule.
I. Small organic molecules
A. Acids
[2,2,2-2H3]acetic acid
[O,2,2,2-2H4]acetic acid
(2S, 3S, 6R)-3-methyllanthionine D-2-aminobutyric acid moiety
MeLanDAb
2-methyl-m-aminobenzoic acid
Me2_maB
2-phenylethyl boronic acid
3-hydroxydecanoyl-2-amino-2(z)-butenoic acid
Dec_dzAb
3-methyl-o-aminobenzoic acid
Me3_oaB
3-phenylpropionic acid
beta-phenylpropionate
D-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid
D_Tic
D-2,4-diaminobutanoic acid
D_Dab
L-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid
Tic
L-2,4-diaminobutanoic acid
Dab
N-acetyl-alpha-amino-isobutyric acid
Ac_Aib
alpha-aminobutyric acid
2-aminobutanoic acid
Abu
alpha-aminoisobutyric acid
Aib
ascorbic acid
benzene boronic acid
epsilon-aminohexanoic acid
6-aminohexanoic acid
eAhx
ethylenediaminetetraacetic acid
EDTA
o-hydroxybenzoic acid
salicylic acid
p-hydroxybenzoic acid
B. Bases
[13C]acetate
C. Others
[15N]formamide
[15N]nitromethane
[4-13C]imidazolyl propionate
acetamide
acetone
acetonitrile
methyl cyanide
chloroform
dioxane
p-dioxane
dioxan
1,4-dioxane
disuccinimidyl suberate
suberic acid bis(N-hydroxy-succinimide ester)
octanedioic acid bis(N-hydroxy-succinimide ester)
dithiothreitol
DTT
glutathione
gamma-glutamylcysteinylglycine
glutathione
gamma-glutamylcysteinylglycine
Gsh
methanol-d3
methanol-d3/d4
methanol-d4
L-stendomycidine
Ste
trifluoroethanol-d2
trifluoroethanol-d3
II. Amino acids and derivatives
A. Alanine
(2S, 3S, 6R)-3-methyllanthionine L-alanine moiety
MeLan_LA
beta-hydroxyoctanoyl-beta-methyl(Z)dehydroalanine
beta-hydroxyoctanoyl-2-amino-2(Z)-butenoic acid
Oct_dzAb
beta-methyl(T)dehydroalanine
2-amino-2(T)-butenoic acid
delta(T)Abu
dtAbu
beta-methyl(Z)dehydroalanine
2-amino-2(Z)-butenoic acid
delta(Z)Abu
dzAbu
D-alanine
L-alaninamide
A_NH2
L-alanine
A
Ala
ala
N-acetyl-L-alanine
Ac_A
N-methyl-L-alanine
Me_A
meso-lanthionine D-alanine moiety
Lan_DA
meso-lanthionine L-alanine moiety
Lan_LA
succinyl-L-alanine
Suc_A
B. Arginine
D-arginine
L-argininamide
R_NH2
L-arginine
R
Arg
arg
L-arginine methyl amide
R_NHCH3
N-acetyl-L-arginine
Ac_R
N-methyl-L-arginine
Me_R
Nh-monomethyl-L-arginine
Nh_Me_R
Nh1,2-sym-dimethyl-L-arginine
Nh_Me2_R
alpha-keto-arginine
2-keto-arginine
2-keto-5-guanidino-pentanoic acid
aKeto_R
C. Aspartic acid
4-(alpha-O-methyl N-glycylglucosaminidyl)-L-aspartic amide
aMGG_D
D-aspartate
L-aspartamide
aspartic 1-amide
D_NH2
L-aspartate
D
Asp
asp
N-acetyl-L-aspartic acid
Ac_D
N-methyl-L-aspartate
Me_D
erythro-hydroxy-L-aspartate
3R-hydroxy-L-aspartate
Hya
D. Asparagine
D-asparagine
L-asparaginamide
N_NH2
L-asparagine
N
Asn
asn
N-acetyl-L-asparagine
Ac_N
N-methyl-L-asparagine
Me_N
E. Cysteine
(acetylamino)methyl L-cysteinamide
Cys(NH2)-Sg-CH2NHCOOH
AcmC_NH2
(acetylamino)methyl L-cysteine
Cys-Sg-CH2NHCOOH
Acm_C
D-cysteine
L-cysteinamide
C_NH2
L-cysteine
C
Cys
cys
N-acetyl-L-cysteine
Ac_C
N-methyl-L-cysteine
Me_C
N-t-butyloxycarbonyl-L-cysteine
(1,1-dimethylethoxy)-carbonyl-L-cysteine
Boc_C
S-5-thio-2-nitrobenzoate L-cysteine
TNB_C
S-t-butyl L-cysteine
t_Bu_C
S-thiomethyl-L-cysteine
Cys-Sg-S-CH3
S_SMe_C
carboxamidomethyl-L-cysteine
Cys-Sg-CH2CONH3
CAM_C
glutathionyl L-cysteine
C_Gsh
F. Glutamic acid
D-glutamate
L-glutamatamide
L-glutamic-1-amide
E_NH2
L-glutamate
E
Glu
glu
N-acetyl-L-glutamic acid
Ac_E
N-methyl-L-glutamate
Me_E
gamma-carboxy-L-glutamate
L-glutamate O5-carboxymethyl ester
Cm_E
gamma-carboxy-glutamic acid
2-amino-4-carboxypentane-dioic acid
Gla
pyroglutamic acid
5-oxo-L-proline
pyrrolidone carboxylic acid
Glp
G. Glutamine
D-glutamine
L-glutaminamide
Q_NH2
L-glutamine
Q
Gln
gln
N-acetyl-L-glutamine
Ac_Q
N-methyl-L-glutamine
Me_Q
pyroglutamic acid
5-oxo-L-proline
pyrrolidone carboxylic acid
Glp
H. Glycine
L-glycine
G
Gly
gly
N-acetylglycine
Ac_G
N-methylglycine
Me_G
N-t-butyloxycarbonyl-glycine
(1,1-dimethylethoxy)-carbonyl-glycine
Boc_G
glycinamide
G_NH2
I. Histidine
1-carboxymethyl L-histidine
pros-carboxymethyl L-histidine
Cm1_H
3-(1-carboxypropyl) L-histidine
tele-(1-carboxypropyl) L-histidine
Cp3_H
3-carboxymethyl L-histidine
tele-carboxymethyl L-histidine
Cm3_H
D-histidine
L-histidinamide
H_NH2
L-histidine
H
His
his
N-acetyl-L-histidine
Ac_H
N-methyl-L-histidine
Me_H
Nt-(1-(4-phenyl-2-(O-seryl)-3S-tosylamidobutan-2-olyl))-L-histidine
PhTsBuSH
Nt-(1-(4-phenyl-3S-tosylamidobutan-2-onyl))-L-histidine
PhTsBu_H
J. Isoleucine
D-alloisoleucine
D_aIle
D-isoleucine
L-alloisoleucine
aIle
L-isoleucinamide
I_NH2
L-isoleucine
I
Ile
ile
N-acetyl-L-isoleucine
Ac_I
N-methyl-L-isoleucine
Me_I
K. Leucine
D-leucine
L-leucinamide
L_NH2
L-leucine
L
Leu
leu
L-leucinol
2-amino-4-methyl-1-pentanol
Leuol
L-norleucine
2-amino-hexanoic acid
Nle
Ahx
N-acetyl-L-leucine
Ac_L
N-methyl-L-leucine
Me_L
N-pyruvoyl-L-leucine
Pyr_L
L. Lysine
4-carboxy-2,6-dinitrophenyl L-lysine
CDNP_K
D-lysine
L-lysinamide
K_NH2
L-lysine
K
Lys
lys
L-lysine lactone
K_lac
N-acetyl-L-lysine
Ac_K
N-methyl-L-lysine
Me_K
N-purine riboside 5'-monophosphate-L-lysine
PMP_K
epsilon-N-trimethyl-L-lysine
N6,N6,N6-trimethyllysine
Tml
M. Methionine
D-methionine
L-methioninamide
M_NH2
L-methionine
M
Met
met
N-acetyl-L-methionine
Ac_M
N-methyl-L-methionine
Me_M
S-(1-(4-phenyl-3S-tosylamidobutan-2-onyl))-L-methionine
PhTsBu_M
N. Ornithine
L-ornithine
Orn
O. Phenylalanine
D-phenylalanine
D-Phe
L-phenylalaninamide
F_NH2
L-phenylalanine
F
Phe
phe
L-phenylalaninol
Phol
N-acetyl-L-phenylalanine
Ac_F
N-methyl-L-phenylalanine
Me_F
N-t-butyloxycarbonyl-L-phenylalanine
(1,1-dimethylethoxy)-carbonyl-L-phenylalanine
Boc_F
P. Proline
D-proline
L-prolinamide
P_NH2
L-proline
P
Pro
pro
N,N-dimethyl-L-proline
Me2_P
N-acetyl-L-proline
Ac_P
N-methyl-L-proline
Me_P
trans-4-hydroxy-L-proline
Hyp
Q. Serine
4'-phosphopantetheinyl-L-serine
S_Ppt
D-serine
L-homoserine
Hse
L-serinamide
S_NH2
L-serine
S
Ser
ser
N-acetyl-L-serine
Ac_S
N-methyl-L-serine
Me_S
O-(1R)-leupeptyl-L-serine
O-(acetylleucylleucyl(1R)argininolyl)-L-serine
LeupepRS
O-(1S)-leupeptyl-L-serine
O-(acetylleucylleucyl(1S)argininolyl)-L-serine
LeupepSS
O-(2-(1-(Nt-histidyl)-4-phenyl-3S-tosylamidobutan-2-olyl))-L-serine
PhTsBuHS
R. Threonine
4-chloro-L-threonine
gamma-chloro-L-threonine
Cl_T
D-allothreonine
D_aThr
D-allothreonine lactone
D_aT_lac
D-threonine
L-allothreonine
aThr
L-threoninamide
T_NH2
L-threonine
T
Thr
thr
N-acetyl-L-threonine
Ac_T
N-methyl-L-threonine
Me_T
S. Tryptophan
D-tryptophan
L-tryptophan
W
Trp
trp
L-tryptophan ethanol amide
W_Etn
L-tryptophanamide
W_NH2
N-acetyl-L-tryptophan
Ac_W
N-methyl-L-tryptophan
Me_W
T. Tyrosine
D-tyrosine
3-iodo-L-tyrosine
Iodo_Y
3-nitro-L-tyrosine
NO2_Y
L-tyrosinamide
Y_NH2
L-tyrosine
Y
Tyr
tyr
L-tyrosine-O-sulfate
Y_SO3H
N-acetyl-L-tyrosine
Ac_Y
N-methyl-L-tyrosine
Me_Y
N-t-butyloxycarbonyl-L-tyrosine
(1,1-dimethylethoxy)-carbonyl-L-tyrosine
Boc_Y
U. Valine
D-valine
L-isovaline
Iva
L-valinamide
V_NH2
L-valine
V
Val
val
N-acetyl-L-valine
Ac_V
N-formyl-L-valine
For_V
N-methyl-L-valine
Me_V
III. Buffers
2-(N-morpholino)propanesulfonic acid
MOPS buffer
HEPES buffer
IV. Hemes
(5,8-2H6)protoheme IX
(7,12-2H6)protoheme
1,2,3,4,5,7,8-heptamethyl-6-propionate-heme
2,3,7,8,12,17,18-heptamethyl-13-propionate-heme
2,4-diisobutyl-deuteroheme
3,8-diisobutenyl-deuteroheme
2,4-dimethyl-deuteroheme
3,8-dimethyl-deuteroheme
(1,3-2H6)protoheme IX
(2,7-2H6)protoheme
(1,8-2H6)protoheme IX
(2,18-2H6)protoheme
2-methyl-4-vinyl-deuteroheme
3-methyl-8-vinyl-deuteroheme
2-methyl-deuteroheme
3-methyl-deuteroheme
4-methyl-2-vinyl-deuteroheme
8-methyl-3-vinyl-deuteroheme
4-methyl-deuteroheme
8-methyl-deuteroheme
6-depropionate-6-methyl-deuteroheme
13-depropionate-13-methyl-protoheme
7-depropionate-7-methyl-deuteroheme
17-depropionate-17-methyl-protoheme
8-mercaptomethyl-protoheme IX
[1,3-2H6]protoheme III
(2,7-2H6)8-methyl-3,7-divinyl-deuteroheme
[1,5-2H6]protoheme III
(2,12-2H6)8-methyl-3,7-divinyl-deuteroheme
[1,5-2H6]protoheme IX
(2,12-2H6)protoheme
[8-2H3]protoheme III
(18-2H3)8-methyl-3,7-divinyl-deuteroheme
[8-2H3]protoheme IX
(18-2H3)protoheme
[alpha,beta,gamma,delta-meso-2H4]protoheme III
(5,10,15,20-2H4)8-methyl-3,7-divinyl-deuteroheme
[alpha,beta,gamma,delta-meso-2H4]protoheme IX
(5,10,15,20-2H4)protoheme
cobalt porphyrin c
2,4-di(alpha-S-cysteinylethyl) cobalt deuteroporphyrinate
3,8-di(alpha-S-cysteinylethyl) cobalt deuteroporphyrinate
deuteroheme
heme c
3,8-di(alpha-S-cysteinylethyl)deuteroheme
isopemptoheme
3-vinyl-deuteroheme
pemptoheme
8-vinyl-deuteroheme
protoheme III
8-methyl-3,7-divinyl-deuteroheme
protoheme IX
protoheme
protoheme XIII
3-methyl-2,8-divinyl-deuteroheme
protoporphyrin IX
zinc(II) porphyrin c
2,4-di(alpha-S-cysteinylethyl) zinc(II) deuteroporphyrinate
3,8-di(alpha-S-cysteinylethyl) zinc(II) deuteroporphyrinate
V. Inorganic molecules
A. Acids
H3PO4
phosphoric acid
B. Metal ions
112Cd 2+
112Cd(II)
113Cd 2+
113Cd(II)
Ca 2+
Ca(II)
Cd 2+
Cd(II)
Co 2+
Co(II)
Cu 1+
Cu(I)
Cu 2+
Cu(II)
Mg 2+
Mg(II)
Ni 2+
Ni(II)
Zn 2+
Zn(II)
C. Others
Cd(ClO4)2
cadmium perchlorate
NaBO3
[15N, 15N]ammonium nitrate
[15N]nitric acid
[15N]ammonium nitrate
[15N]ammonium chloride
[15N]ammonium sulfate
azide
boronic acid
calcium chloride
CaCl2
carbon disulfide
CS2
carbon monoxide
CO
dimethylsulfoxide-d6
DMSO-d6
hexamethyldisiloxane
HMS
liquid ammonia
liquid NH3
oxygen
O2
phosphate buffer
potassium chloride
potassium ferricyanide
potassium phosphate buffer
sodium chloride
NaCl
sodium dithionite
sodium phosphate buffer
cyanide
tetramethylammonium nitrate
trimethyl phosphine
PMe3
water
[1H2]H2O
[1H]water
H2O
VI. NMR Chemical shift standards
3-(trimethylsilyl)-propane-sulfonic acid
DSS
4,4-dimethylsilapentane-1-sulfonate
4,4-dimethyl-4-silapentane-1-sulfonate
2,2-dimethyl-2-silapentane-5-sulfonate
(trimethylsilyl)propane sulfonic acid
2,2,2-trimethyl-2-silapentane-5-sulfonate
4,4-dimethyl-4-silapentane-1-sulfonic acid
sodium 2,2-dimethyl-2-silapentane-5-sulfonate
sodium 3-(trimethylsilyl)propane sulfonate
TMSPS
3-(trimethylsilyl)propane sulfonic acid sodium salt
2,2-dimethyl-2-silapentane sulfonic acid sodium salt
sodium 4,4-dimethyl[2,2,3,3-2H4]-4-silapentanoate
TSP
sodium 3-trimethylsilyl-[2,2,3,3-2H4]propionate
sodium 3-(trimethylsilyl)-1-[2H4]propanoate
3-trimethylsilyl-[2,2,3,3-d4]propionic acid
sodium-2,2,3,3-tetradeutero-3-trimethylsilylpropionate
(trimethylsilyl)-propionic-d4 acid sodium salt
trimethylsilylpropionate
tetramethylsilane
TMS
(CH3)4Si
VII. Nucleotides
P1,P5-bis(5'-adenosyl)pentaphosphate
AP5A
adenosine 2',5'-diphosphate
2',5'-ADP
adenosine 5'-monophosphate
AMP
adenosine 5'-triphosphate
ATP
cytidine 2'-monophosphate
2' CMP
cytidine 3'-monophosphate
3' CMP
dehydroalanine
2-amino-2-propenoic acid
Delta_A
guanosine
guanosine 2'-monophosphate
2' GMP
guanosine 3'-monophosphate
3' GMP
guanosine 5'-diphosphate
GDP
guanosine 5'-monophosphate
5' GMP
guanosine 5'-triphosphate
GTP
uridine 2'-monophosphate
2' UMP
uridine 3'-monophosphate
3' UMP
VIII. Prosthetic groups, cofactors, and inhibitors
[1'-13C]6,7-dimethyl-8-ribityllumazine
[1,3,4-15N3]flavin adenine dinucleotide
[1,3,5-15N3]FAD
[1,3,5,10-15N4]flavin adenine dinucleotide
[1,3,5,10-15N4]FAD
[1,3,5,10-15N4]riboflavin 5'-phosphate
[1,3,5,10-15N4]flavin mononucleotide
[1,3,5,10-15N4]FMN
[1,3,5,8-15N4]6,7-dimethyl-8-ribityllumazine
[2,4a-13C2]flavin adenine dinucleotide
[2,4a-13C2]FAD
[2,4a-13C2]riboflavin 5'-phosphate
[2,4a-13C2]flavin mononucleotide
[2,4a-13C2]FMN
[2-13C]flavin adenine dinucleotide
[2-13C]FAD
[2Fe-2S]
[4,10a-13C2]flavin adenine dinucleotide
[4,10a-13C2]FAD
[4,10a-13C2]riboflavin 5'-phosphate
[4,10a-13C2]flavin mononucleotide
[4,10a-13C2]FMN
[4-13C]beta-nicotinamide adenine dinucleotide
[4-13C]NAD
[4-13C]nicotinamide adenine dinucleotide
[4a-13C]flavin adenine dinucleotide
[41-13C]FAD
[6,7-13C2]6,7-dimethyl-8-ribityllumazine
[6,8alpha-13C2]riboflavin 5'-phosphate
[6,8alpha-13C2]flavin mononucleotide
[6,8alpha-13C2]FMN
[6alpha,7alpha-13C2]6,7-dimethyl-8-ribityllumazine
[7alpha,9-13C2]riboflavin 5'-phosphate
[7alpha,9-13C2]flavin mononucleotide
[7alpha,9-13C2]FMN
[8-15N]6,7-dimethyl-8-ribityllumazine
beta-nicotinamide adenine dinucleotide phosphate
nicotinamide adenine dinucleotide phosphate
NADP+
beta-nicotinamide adenine dinucleotide phosphate, reduced
NADPH
nicotinamide adenine dinucleotide phosphate, reduced
1,2-dimyrostoyl-sn-glycero-3-phosphocholine
3-phosphoglycerate
4'-phosphopantetheine
folic acid
pteroylglutamic acid
methotrexate
myo-inositol hexakis[dihydrogen phosphate]
inositol hexaphosphate
perdeuterated dodecylphosphocholine
thymidine 3',5'-bisphosphate
pdTp
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