FAIRMol

KB_Leish_119

Pose ID 3516 Compound 2422 Pose 130

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
T06
T. brucei DHFR T. brucei
Ligand KB_Leish_119
PDB8RHT↗

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 high Native strong SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.00
Burial
95%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>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 (-0.639 kcal/mol/HA) ✓ Good fit quality (FQ -5.72) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (17.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Internal clashes (9)
Score
-15.332
kcal/mol
LE
-0.639
kcal/mol/HA
Fit Quality
-5.72
FQ (Leeson)
HAC
24
heavy atoms
MW
343
Da
LogP
2.11
cLogP
Final rank
0.6710
rank score
Inter norm
-0.942
normalised
Contacts
18
H-bonds 1
Strain ΔE
17.0 kcal/mol
SASA buried
95%
Lipo contact
86% BSA apolar/total
SASA unbound
613 Ų
Apolar buried
503 Ų

Interaction summary

HBD 1 HY 10 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap15Native recall0.71
Jaccard0.62RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
130 0.6710015680972891 -0.942234 -15.332 1 18 15 0.71 0.00 - no Current
108 1.8147398157015295 -0.96444 -18.8902 3 11 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -15.332kcal/mol
Ligand efficiency (LE) -0.6388kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.725
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 343.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.11
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 1.62kcal/mol
Minimised FF energy -15.42kcal/mol

SASA & burial

✓ computed
SASA (unbound) 613.3Ų
Total solvent-accessible surface area of free ligand
BSA total 585.1Ų
Buried surface area upon binding
BSA apolar 503.4Ų
Hydrophobic contacts buried
BSA polar 81.7Ų
Polar contacts buried
Fraction buried 95.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1763.3Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 575.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)