plinderp.doi.bio/plinder/1erm

Protein Data Bank Entry: 1ERM

plinder/1erm.json

General Information

• PDB ID: 1ERM
• Release Date: April 6, 2000
• Oligomeric State: Monomeric
• Method of Determination: X-ray Diffraction
• Keywords: Hydrolase
• pH: 8.0
• Resolution: 1.7 Å

Structure Details

Ligands

Ligand: BJI

• Chain ID: B
• SMILES Notation: CC(=O)NC@@Hc1)B(O)O
• Molecular Weight: 251.10 Da
• Covalent Linkages:
• 70:SER:A:45:OG - 500:BJI:B:.:B
• Chemistry Information:
• Number of Rotatable Bonds: 5
• Hydrogen Bond Donors: 4
• Hydrogen Bond Acceptors: 4
• Number of Rings: 1
• Total Heavy Atoms: 18
• Properties:
• TPSA: 106.86
• QED Score: 0.5248
• ClogP: -0.556

Systems

System 1ERM:1:1.A:1.B

• Biounit ID: 1
• Ligand Involved: BJI
• Crystal Validation:
• Number of Ligand Resolved Heavy Atoms: 18
• Percent Processed Residues: 100%
• Average B Factor: 17.29

Validation Metrics

• Resolution: 1.7 Å
• R Value: 0.18
• Clashscore: 5.62
• MolProbity Score: 2.02
• Atom Count: 2183
• Mean B Factor: 22.79

Sequence Information

• Chain A Sequence (SEQRES): HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW

Water Chains

• Chains Representing Water Molecules: C

Structural Features and Validations

• Pass Criteria: The overall structure has passed validation checks.
• Percent Ramachandran Outliers: 0.0%
• Percent Rotamer Outliers: 8.8%
• MolProbity Validation: Comprehensive geometry validation indicates no significant issues with stereochemistry, bond lengths, and angles.

Ligand Information Overview

General Information

• PDB ID: 1erm
• Chain Identifier: B
• Chemical Component ID (CCD): BJI
• Ligand Name: Not specified
• Molecular Weight: 251.096502948 g/mol
• SMILES: CC(=O)N[C@@H](Cc1cccc(C(=O)O)c1)B(O)O
• Resolved SMILES: CC(=O)N[C@H](B(O)O)Cc1cccc(c1)C(=O)O
• RDKit Canonical SMILES: CC(=O)N[C@@H](Cc1cccc(C(=O)O)c1)B(O)O
• InChI Crystal: InChI=1S/C11H14BNO5/c1-7(14)13-10(12(17)18)6-8-3-2-4-9(5-8)11(15)16/h2-5,10,17-18H,6H2,1H3,(H,13,14)(H,15,16)/t10-/m0/s1

Structural Characteristics

• Total Polarity Surface Area (TPSA): 106.86 Ų
• Number of Rotatable Bonds: 5
• Hydrogen Bond Donors (HBD): 4
• Hydrogen Bond Acceptors (HBA): 4
• Number of Rings: 1
• Number of Heavy Atoms: 18
• Covalent Linkage: Yes
• Covalently linked to residue: SER 45 (OG atom)

Interactions

The ligand has various interactions with the protein structure:

• Interacting Residues:
• Chain A:
  • SER 45 (Hydrogen bonds, protein as donor)
  • ASN 107 (Hydrogen bonds, protein as donor)
  • ALA 145 (Hydrogen bonds, mixed polarity)
  • SER 80 (Hydrophobic contacts, pi-stacking)
  • THR 212 (Hydrophobic contacts, multiple hydrogen bonds)
  • LYS 209/218 (Salt bridges, protein as donor)
• Interacting Waters: Not specified in detail

Validation and Quality Measures

• Sanitization Checks: Passed
• All Atoms Connected: Yes
• Molecular Formula Validation: Yes
• Stereochemistry Preserved: Yes
• Minimum Distance to Waters: 2.86 Å
• Volume Overlap with Protein: 0.0731

Additional Properties

• Is Covalent Link Active: True
• Is Lipinski Compliant: Yes
• Posebusters Result: Successful with criteria such as bond angles, bond lengths, and stereochemistry checks passed.
• Average B-factor: 17.29
• Ligand Type: Small Molecule

This ligand is a covalently bonded small molecule with a considerable number of interactions within the protein pocket of the X-ray diffraction structure with ID 1erm. It adheres to Lipinski's rules, suggesting drug-likeness and has passed various validation checks confirming its pose and configuration.