The Peptide Palv1.0
Bioluminescent 3D Lab
Biochemical Structure Index

Molecule Library

Explore 29 curated biomolecules across amino acids, lipids, carbohydrates, and reference proteins.

Category:
Polarity:

Alanine

ALA (A)
C3H7NO2 • 89.09 g/mol
amino acid

Simplest chiral amino acid with a methyl side chain. Abundant in proteins and key in the glucose-alanine cycle.

Polaritynonpolar
Charge pH 7neutral
pI Point6.00
#nonpolar#hydrophobic#aliphatic
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Valine

VAL (V)
C5H11NO2 • 117.15 g/mol
amino acid

Branched-chain amino acid with an isopropyl side chain. Important for muscle metabolism and tissue repair.

Polaritynonpolar
Charge pH 7neutral
pI Point5.96
#nonpolar#hydrophobic#aliphatic#branched-chain
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Leucine

LEU (L)
C6H13NO2 • 131.17 g/mol
amino acid

Essential branched-chain amino acid that directly stimulates mammalian target of rapamycin (mTOR) protein synthesis.

Polaritynonpolar
Charge pH 7neutral
pI Point5.98
#nonpolar#hydrophobic#aliphatic#branched-chain
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Isoleucine

ILE (I)
C6H13NO2 • 131.17 g/mol
amino acid

Isomer of leucine with two stereocenters. Essential for hemoglobin synthesis and energy regulation.

Polaritynonpolar
Charge pH 7neutral
pI Point6.02
#nonpolar#hydrophobic#aliphatic#essential
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Proline

PRO (P)
C5H9NO2 • 115.13 g/mol
amino acid

Unique cyclic amino acid with a secondary amine (imino acid). Induces bends and kinks in protein alpha-helices.

Polaritynonpolar
Charge pH 7neutral
pI Point6.48
#nonpolar#hydrophobic#cyclic#helix-breaker
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Phenylalanine

PHE (F)
C9H11NO2 • 165.19 g/mol
amino acid

Highly hydrophobic aromatic amino acid containing a benzyl side chain; precursor to tyrosine and neurotransmitters.

Polaritynonpolar
Charge pH 7neutral
pI Point5.48
#nonpolar#hydrophobic#aromatic#essential
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Methionine

MET (M)
C5H11NO2S • 149.21 g/mol
amino acid

Sulfur-containing essential amino acid; universal initiating amino acid in eukaryotic protein synthesis (AUG codon).

Polaritynonpolar
Charge pH 7neutral
pI Point5.74
#nonpolar#hydrophobic#sulfur#initiator
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Tryptophan

TRP (W)
C11H12N2O2 • 204.23 g/mol
amino acid

Largest amino acid with a bicyclic indole ring. Exhibits intrinsic protein fluorescence and serves as serotonin precursor.

Polaritynonpolar
Charge pH 7neutral
pI Point5.89
#nonpolar#hydrophobic#aromatic#fluorescent
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Glycine

GLY (G)
C2H5NO2 • 75.07 g/mol
amino acid

Smallest amino acid with a single hydrogen atom side chain; only achiral amino acid, providing immense peptide backbone flexibility.

Polaritynonpolar
Charge pH 7neutral
pI Point5.97
#nonpolar#achiral#tiny#flexible
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Cysteine

CYS (C)
C3H7NO2S • 121.16 g/mol
amino acid

Contains a reactive thiol (-SH) group capable of forming covalent disulfide bonds crucial for protein tertiary structure.

Polaritynonpolar
Charge pH 7neutral
pI Point5.07
#thiol#disulfide#reactive
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Serine

SER (S)
C3H7NO3 • 105.09 g/mol
amino acid

Polar amino acid with a primary alcohol; frequently phosphorylated in cell signaling and present in catalytic triads.

Polaritypolar uncharged
Charge pH 7neutral
pI Point5.68
#polar#hydrophilic#alcohol#phosphorylation
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Threonine

THR (T)
C4H9NO3 • 119.12 g/mol
amino acid

Contains a secondary alcohol and two stereocenters. Major site of O-linked glycosylation and phosphorylation.

Polaritypolar uncharged
Charge pH 7neutral
pI Point5.60
#polar#hydrophilic#alcohol#essential
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Tyrosine

TYR (Y)
C9H11NO3 • 181.19 g/mol
amino acid

Aromatic amino acid with a phenolic hydroxyl group. Target for receptor tyrosine kinases and precursor to catecholamines.

Polaritypolar uncharged
Charge pH 7neutral
pI Point5.66
#polar#hydrophilic#aromatic#signaling
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Asparagine

ASN (N)
C4H8N2O3 • 132.12 g/mol
amino acid

Carboxamide-bearing derivative of aspartate; primary consensus site for N-linked glycosylation (Asn-X-Ser/Thr).

Polaritypolar uncharged
Charge pH 7neutral
pI Point5.41
#polar#hydrophilic#amide#glycosylation
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Glutamine

GLN (Q)
C5H10N2O3 • 146.15 g/mol
amino acid

Most abundant free amino acid in human blood. Key nitrogen donor for purine and pyrimidine biosynthesis.

Polaritypolar uncharged
Charge pH 7neutral
pI Point5.65
#polar#hydrophilic#amide#nitrogen-transport
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Lysine

LYS (K)
C6H14N2O2 • 146.19 g/mol
amino acid

Basic amino acid with a flexible butylamino side chain; carries positive charge at pH 7.4. Major histone methylation site.

Polaritypositively charged
Charge pH 7positive
pI Point9.74
#charged#basic#positively_charged#essential
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Arginine

ARG (R)
C6H14N4O2 • 174.2 g/mol
amino acid

Highly basic amino acid with a resonance-stabilized guanidinium group (pKa ~12.5), consistently protonated at physiological pH.

Polaritypositively charged
Charge pH 7positive
pI Point10.76
#charged#basic#positively_charged#guanidinium
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Histidine

HIS (H)
C6H9N3O2 • 155.15 g/mol
amino acid

Aromatic imidazole side chain with near-neutral pKa (~6.0); acts as versatile general acid-base catalyst in enzymes.

Polaritypositively charged
Charge pH 7positive
pI Point7.59
#charged#basic#aromatic#catalytic
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Aspartic Acid

ASP (D)
C4H7NO4 • 133.1 g/mol
amino acid

Dicarboxylic amino acid; fully deprotonated as aspartate at physiological pH. Critical for coordinating catalytic metal cations.

Polaritynegatively charged
Charge pH 7negative
pI Point2.77
#charged#acidic#negatively_charged
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Glutamic Acid

GLU (E)
C5H9NO4 • 147.13 g/mol
amino acid

Carboxylate side chain acting as major excitatory neurotransmitter (glutamate) in the central nervous system.

Polaritynegatively charged
Charge pH 7negative
pI Point3.22
#charged#acidic#negatively_charged#neurotransmitter
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Cholesterol

C27H46O • 386.65 g/mol
lipid

Essential polycyclic amphipathic sterol modulating eukaryotic plasma membrane fluidity and steroid precursor.

#lipid#sterol#membrane#amphipathic
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Dipalmitoylphosphatidylcholine (DPPC)

C40H80NO8P • 734.04 g/mol
lipid

Major phospholipid component of pulmonary surfactant preventing alveolar collapse during respiration.

#lipid#phospholipid#surfactant#bilayer
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Palmitic Acid

C16H32O2 • 256.42 g/mol
lipid

16-carbon saturated fatty acid; first fatty acid produced during lipogenesis in animals.

#lipid#fatty-acid#saturated
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D-Glucose

C6H12O6 • 180.16 g/mol
carbohydrate

Primary hexose monosaccharide and energy currency of cellular glycolysis and respiration.

#carbohydrate#monosaccharide#hexose#glycolysis
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D-Ribose

C5H10O5 • 150.13 g/mol
carbohydrate

Aldopentose sugar forming the central structural backbone of ribonucleic acid (RNA) and ATP.

#carbohydrate#pentose#nucleotide-backbone
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Sucrose

C12H22O11 • 342.3 g/mol
carbohydrate

Non-reducing disaccharide composed of alpha-D-glucopyranose and beta-D-fructofuranose linked by an alpha-1,2-glycosidic bond.

#carbohydrate#disaccharide#glycosidic-bond
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Crambin

Polypeptide (46 residues) • 4716 g/mol
protein

Small seed storage plant protein from Crambe abyssinica. High-resolution benchmark model containing 3 disulfide bonds.

#protein#plant#disulfide#high-resolution
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Green Fluorescent Protein (GFP)

Polypeptide (238 residues) • 26890 g/mol
protein

Beta-barrel protein from Aequorea victoria exhibiting bioluminescent green fluorescence via an autocatalytic Ser65-Tyr66-Gly67 chromophore.

#protein#bioluminescent#beta-barrel#chromophore
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Insulin (2-Chain Monomer)

Polypeptide (51 residues) • 5808 g/mol
protein

Essential peptide hormone regulating carbohydrate and fat metabolism, composed of A and B chains linked by two interchain disulfide bonds.

#protein#hormone#peptide#disulfide
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