Compound Profile Skill
Comprehensive compound analysis for drug discovery and medicinal chemistry.
Quick Start
/compound erlotinib
/compound-profile CC1=CC=C(C=C1)CNC(=O)C1=NC=C(C=C1)N
Analyze osimertinib properties and bioactivity
Compare gefitinib, erlotinib, afatinib profiles
What's Included
| Section |
Description |
Data Source |
| Basic Info |
Name, type, status, company |
ChEMBL, DrugBank |
| Structure |
SMILES, InChI, molecular weight |
PubChem, ChEMBL |
| Properties |
LogP, HBD, HBA, TPSA, RO5 |
Calculated, PubChem |
| Bioactivity |
Target affinity, IC50, Ki |
ChEMBL, BindingDB |
| Development |
Phase, indications, status |
Drugs@FDA |
| Similar Compounds |
Structure similarity search |
ChEMBL |
| Safety |
Known toxicity, warnings |
SIDER, PubChem |
Output Structure
# Compound Profile: Erlotinib
## Executive Summary
Erlotinib is a first-generation EGFR TKI approved for NSCLC (2004).
Key characteristics: Oral bioavailability, good brain penetration,
resistance mutations limit long-term efficacy.
## Basic Information
| Field | Value |
|-------|-------|
| Name | Erlotinib |
| Brand Names | Tarceva |
| ChEMBL ID | CHEMBL880 |
| Type | Small molecule |
| Class | Kinase inhibitor |
| Status | Approved |
| Approval Year | 2004 |
| Company | Astellas (OSI) |
| Indications | NSCLC, pancreatic cancer |
## Structure & Properties
**SMILES:** `COc1cc2nc(Nc3ccc(Oc4ccc(O)cc4)cc3)nc2cc1OC`
| Property | Value | Rule of 5 Check |
|----------|-------|----------------|
| MW | 393.4 Da | ✓ (<500) |
| LogP | 3.1 | ✓ (<5) |
| HBD | 1 | ✓ (≤5) |
| HBA | 7 | ✓ (≤10) |
| TPSA | 76.3 Ų | ✓ (<140) |
| Rotatable Bonds | 6 | |
## Bioactivity
| Target | Type | Affinity | Units |
|--------|------|----------|-------|
| EGFR | IC50 | 0.5 | nM |
| ERBB2 | IC50 | 1200 | nM |
| LCK | IC50 | 5 | nM |
## Development History
| Year | Milestone |
|------|-----------|
| 2004 | FDA Approval (NSCLC) |
| 2005 | EMEA Approval |
| 2010 | Pancreatic cancer approval |
| 2011 | Generic launch (US) |
## Similar Compounds
| Compound | Similarity | Difference |
|----------|------------|------------|
| Gefitinib | 85% | Different core scaffold |
| Afatinib | 72% | Irreversible binder |
| Osimertinib | 68% | 3rd-gen, mutant-selective |
| Icotinib | 82% | China-approved analog |
## Safety Profile
**Common AEs:** Rash, diarrhea, fatigue, anorexia
**Boxed Warning:** Interstitial lung disease
**Contraindications:** Hypersensitivity to erlotinib
## Patent Status
| Patent | Number | Expiry |
|--------|---------|--------|
| Base patent | US5747498 | 2019 (expired) |
| Formulation | US6943129 | 2020 |
| Method of use | US6900221 | 2021 |
Examples
By Name
/compound erlotinib
/compound-profile sotorasib
By Structure
/compound "CC1=CC=C(C=C1)CNC(=O)C1=NC=C(C=C1)N"
/compound-profile SMILES
Comparison
Compare compounds erlotinib, gefitinib, afatinib
Analyze bioactivity across EGFR inhibitors
Property Analysis
/compound erlotinib --focus properties
Analyze drug-likeness of this compound
Check Lipinski rule of 5 violations
Running Scripts
# Fetch compound by name
python scripts/fetch_compound_data.py erlotinib --output compound.json
# Fetch by SMILES
python scripts/fetch_compound_data.py --smiles "CC1=CC=C..." -o data.json
# Similarity search
python scripts/fetch_compound_data.py --similar CHEMBL880 --threshold 0.7
# Bioactivity summary
python scripts/fetch_compound_data.py erlotinib --bioactivity -o activity.json
# Structure search
python scripts/fetch_compound_data.py --scaffold quinazoline --limit 20
Requirements
pip install requests pandas rdkit
Additional Resources
- ChEMBL API Reference
- PubChem API
- Property Calculation
Best Practices
- Use standard names: Generic names preferred over brand
- Verify ChEMBL ID: Most reliable identifier
- Check bioactivity: Cross-reference multiple sources
- Analog analysis: Use similarity searches for SAR
- Validate SMILES: Check structure validity
Common Pitfalls
| Pitfall |
Solution |
| Name ambiguity |
Use ChEMBL ID when possible |
| Stereochemistry |
SMILES may not capture isomerism |
| Outdated data |
Check multiple sources |
| Salt forms |
API may have multiple entries |
| Tautomerism |
Different SMILES for same structure |
1---2name: compound-profile3description: Generate comprehensive compound profiles including structure, properties, bioactivity, and development status. Use for drug analysis, SAR studies, and competitive profiling. Keywords: compound, drug, molecule, structure, SMILES, bioactivity, IC504---5
6# Compound Profile Skill
7
8Comprehensive compound analysis for drug discovery and medicinal chemistry.
9
10## Quick Start
11
12```
13/compound erlotinib
14/compound-profile CC1=CC=C(C=C1)CNC(=O)C1=NC=C(C=C1)N
15Analyze osimertinib properties and bioactivity
16Compare gefitinib, erlotinib, afatinib profiles
17```
18
19## What's Included
20
21| Section | Description | Data Source |
22|---------|-------------|-------------|
23| Basic Info | Name, type, status, company | ChEMBL, DrugBank |
24| Structure | SMILES, InChI, molecular weight | PubChem, ChEMBL |
25| Properties | LogP, HBD, HBA, TPSA, RO5 | Calculated, PubChem |
26| Bioactivity | Target affinity, IC50, Ki | ChEMBL, BindingDB |
27| Development | Phase, indications, status | Drugs@FDA |
28| Similar Compounds | Structure similarity search | ChEMBL |
29| Safety | Known toxicity, warnings | SIDER, PubChem |
30
31## Output Structure
32
33```markdown
34# Compound Profile: Erlotinib
35
36## Executive Summary
37Erlotinib is a first-generation EGFR TKI approved for NSCLC (2004).
38Key characteristics: Oral bioavailability, good brain penetration,
39resistance mutations limit long-term efficacy.
40
41## Basic Information
42| Field | Value |
43|-------|-------|
44| Name | Erlotinib |
45| Brand Names | Tarceva |
46| ChEMBL ID | CHEMBL880 |
47| Type | Small molecule |
48| Class | Kinase inhibitor |
49| Status | Approved |
50| Approval Year | 2004 |
51| Company | Astellas (OSI) |
52| Indications | NSCLC, pancreatic cancer |
53
54## Structure & Properties
55**SMILES:** `COc1cc2nc(Nc3ccc(Oc4ccc(O)cc4)cc3)nc2cc1OC`
56
57| Property | Value | Rule of 5 Check |
58|----------|-------|----------------|
59| MW | 393.4 Da | ✓ (<500) |
60| LogP | 3.1 | ✓ (<5) |
61| HBD | 1 | ✓ (≤5) |
62| HBA | 7 | ✓ (≤10) |
63| TPSA | 76.3 Ų | ✓ (<140) |
64| Rotatable Bonds | 6 | |
65
66## Bioactivity
67
68| Target | Type | Affinity | Units |
69|--------|------|----------|-------|
70| EGFR | IC50 | 0.5 | nM |
71| ERBB2 | IC50 | 1200 | nM |
72| LCK | IC50 | 5 | nM |
73
74## Development History
75| Year | Milestone |
76|------|-----------|
77| 2004 | FDA Approval (NSCLC) |
78| 2005 | EMEA Approval |
79| 2010 | Pancreatic cancer approval |
80| 2011 | Generic launch (US) |
81
82## Similar Compounds
83| Compound | Similarity | Difference |
84|----------|------------|------------|
85| Gefitinib | 85% | Different core scaffold |
86| Afatinib | 72% | Irreversible binder |
87| Osimertinib | 68% | 3rd-gen, mutant-selective |
88| Icotinib | 82% | China-approved analog |
89
90## Safety Profile
91**Common AEs:** Rash, diarrhea, fatigue, anorexia
92**Boxed Warning:** Interstitial lung disease
93**Contraindications:** Hypersensitivity to erlotinib
94
95## Patent Status
96| Patent | Number | Expiry |
97|--------|---------|--------|
98| Base patent | US5747498 | 2019 (expired) |
99| Formulation | US6943129 | 2020 |
100| Method of use | US6900221 | 2021 |
101```
102
103## Examples
104
105### By Name
106```
107/compound erlotinib
108/compound-profile sotorasib
109```
110
111### By Structure
112```
113/compound "CC1=CC=C(C=C1)CNC(=O)C1=NC=C(C=C1)N"
114/compound-profile SMILES
115```
116
117### Comparison
118```
119Compare compounds erlotinib, gefitinib, afatinib
120Analyze bioactivity across EGFR inhibitors
121```
122
123### Property Analysis
124```
125/compound erlotinib --focus properties
126Analyze drug-likeness of this compound
127Check Lipinski rule of 5 violations
128```
129
130## Running Scripts
131
132```bash
133# Fetch compound by name
134python scripts/fetch_compound_data.py erlotinib --output compound.json
135
136# Fetch by SMILES
137python scripts/fetch_compound_data.py --smiles "CC1=CC=C..." -o data.json
138
139# Similarity search
140python scripts/fetch_compound_data.py --similar CHEMBL880 --threshold 0.7
141
142# Bioactivity summary
143python scripts/fetch_compound_data.py erlotinib --bioactivity -o activity.json
144
145# Structure search
146python scripts/fetch_compound_data.py --scaffold quinazoline --limit 20
147```
148
149## Requirements
150
151```bash
152pip install requests pandas rdkit
153```
154
155## Additional Resources
156
157- [ChEMBL API Reference](reference/chembl-api.md)
158- [PubChem API](reference/pubchem-api.md)
159- [Property Calculation](reference/properties.md)
160
161## Best Practices
162
1631. **Use standard names**: Generic names preferred over brand
1642. **Verify ChEMBL ID**: Most reliable identifier
1653. **Check bioactivity**: Cross-reference multiple sources
1664. **Analog analysis**: Use similarity searches for SAR
1675. **Validate SMILES**: Check structure validity
168
169## Common Pitfalls
170
171| Pitfall | Solution |
172|---------|----------|
173| Name ambiguity | Use ChEMBL ID when possible |
174| Stereochemistry | SMILES may not capture isomerism |
175| Outdated data | Check multiple sources |
176| Salt forms | API may have multiple entries |
177| Tautomerism | Different SMILES for same structure |
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