FAIRMol

KB_Leish_33

Pose ID 13024 Compound 387 Pose 145

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand KB_Leish_33
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
22.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.45, H-bond role recall 0.00
Burial
46%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
2 protein-contact clashes 74% of hydrophobic surface is solvent-exposed (17/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.567 kcal/mol/HA) ✓ Good fit quality (FQ -5.63) ✓ Good H-bonds (4 bonds) ✓ Good burial (46% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (22.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-18.721
kcal/mol
LE
-0.567
kcal/mol/HA
Fit Quality
-5.63
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
2.91
cLogP
Final rank
4.0941
rank score
Inter norm
-0.584
normalised
Contacts
8
H-bonds 5
Strain ΔE
22.7 kcal/mol
SASA buried
46%
Lipo contact
70% BSA apolar/total
SASA unbound
723 Ų
Apolar buried
233 Ų

Interaction summary

HBD 1 HBA 3 HY 2 PI 0 CLASH 2

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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.45RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:221

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:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
94 0.983913686264644 -0.858335 -27.6464 6 15 0 0.00 0.00 - no Open
151 2.273298104065473 -0.846275 -25.1995 3 17 0 0.00 0.00 - no Open
142 2.946945609023217 -0.993841 -28.3916 2 17 0 0.00 0.00 - no Open
122 3.1529463375870637 -0.703753 -17.4509 7 15 0 0.00 0.00 - no Open
128 3.6405601809908945 -0.837547 -23.8296 6 19 0 0.00 0.00 - no Open
115 3.9252777073304115 -0.788301 -27.0966 5 13 0 0.00 0.00 - no Open
145 4.094128194450695 -0.584234 -18.7207 5 8 5 0.62 0.00 - no Current
97 4.175623452188693 -0.858805 -25.7709 12 20 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 -18.721kcal/mol
Ligand efficiency (LE) -0.5673kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.629
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 459.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.91
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -124.01kcal/mol
Minimised FF energy -146.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 722.6Ų
Total solvent-accessible surface area of free ligand
BSA total 330.6Ų
Buried surface area upon binding
BSA apolar 233.2Ų
Hydrophobic contacts buried
BSA polar 97.5Ų
Polar contacts buried
Fraction buried 45.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3027.1Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1562.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)