FAIRMol

KB_chagas_123

Pose ID 8241 Compound 3976 Pose 111

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand KB_chagas_123
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
12.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.76, H-bond role recall 0.43
Burial
84%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.158 kcal/mol/HA) ✓ Good fit quality (FQ -10.22) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (12.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-26.634
kcal/mol
LE
-1.158
kcal/mol/HA
Fit Quality
-10.22
FQ (Leeson)
HAC
23
heavy atoms
MW
303
Da
LogP
3.14
cLogP
Final rank
1.8358
rank score
Inter norm
-1.247
normalised
Contacts
18
H-bonds 10
Strain ΔE
12.8 kcal/mol
SASA buried
84%
Lipo contact
81% BSA apolar/total
SASA unbound
583 Ų
Apolar buried
397 Ų

Interaction summary

HBD 1 HBA 6 HY 2 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap16Native recall0.84
Jaccard0.76RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
111 1.8358001927634409 -1.24655 -26.6342 10 18 16 0.84 0.43 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -26.634kcal/mol
Ligand efficiency (LE) -1.1580kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.220
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 303.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.14
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 62.62kcal/mol
Minimised FF energy 49.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 583.4Ų
Total solvent-accessible surface area of free ligand
BSA total 488.0Ų
Buried surface area upon binding
BSA apolar 396.8Ų
Hydrophobic contacts buried
BSA polar 91.2Ų
Polar contacts buried
Fraction buried 83.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2547.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1404.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)