FAIRMol

KB_Leish_139

Pose ID 9612 Compound 2885 Pose 126

DB SELECTIONDocking 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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand KB_Leish_139
PDB9IFF↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
45.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.69, Jaccard 0.43
Burial
74%
Hydrophobic fit
75%
Reason: strain 45.8 kcal/mol
strain ΔE 45.8 kcal/mol 4 protein-contact clashes 4 intramolecular clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.563
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.418
ADMET + ECO + DL
ADMETscore (GDS)
0.362
absorption · distr. · metab.
DLscore
0.431
drug-likeness
P(SAFE)
0.09
GDS classification
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.508 kcal/mol/HA) ✓ Good fit quality (FQ -5.04) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (45.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-16.759
kcal/mol
LE
-0.508
kcal/mol/HA
Fit Quality
-5.04
FQ (Leeson)
HAC
33
heavy atoms
MW
486
Da
LogP
4.13
cLogP
Final rank
2.9673
rank score
Inter norm
-0.836
normalised
Contacts
17
H-bonds 5
Strain ΔE
45.8 kcal/mol
SASA buried
74%
Lipo contact
75% BSA apolar/total
SASA unbound
773 Ų
Apolar buried
428 Ų

Interaction summary

HBA 3 HY 11 PI 0 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap9Native recall0.69
Jaccard0.43RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
484 1.6830606252738989 -0.743187 -19.2115 5 14 0 0.00 - - no Open
124 1.9789215848404698 -0.917724 -24.5812 5 18 0 0.00 - - no Open
457 2.5136273279812995 -0.919656 -24.9115 5 18 0 0.00 - - no Open
110 2.8793248649702754 -0.805397 -25.4557 5 15 0 0.00 - - no Open
126 2.9672521965662164 -0.835595 -16.7586 5 17 9 0.69 - - no Current
535 3.304468521208352 -0.813519 -25.9782 5 15 0 0.00 - - no Open
97 3.503518404096005 -1.01121 -27.3035 4 21 0 0.00 - - no Open
473 3.7845323780093345 -0.749603 -15.8986 7 17 0 0.00 - - no Open
484 4.235486935676271 -1.01852 -28.93 6 19 0 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 -16.759kcal/mol
Ligand efficiency (LE) -0.5078kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.039
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 485.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.13
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 120.72kcal/mol
Minimised FF energy 74.96kcal/mol

SASA & burial

✓ computed
SASA (unbound) 773.1Ų
Total solvent-accessible surface area of free ligand
BSA total 571.5Ų
Buried surface area upon binding
BSA apolar 428.3Ų
Hydrophobic contacts buried
BSA polar 143.2Ų
Polar contacts buried
Fraction buried 73.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3081.6Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1526.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)