FAIRMol

Z32661458

Pose ID 13357 Compound 206 Pose 478

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z32661458
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
29.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.40, H-bond role recall 1.00
Burial
55%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
2 protein-contact clashes 38% of hydrophobic surface appears solvent-exposed (10/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.479 kcal/mol/HA) ✓ Good fit quality (FQ -4.86) ✓ Good H-bonds (4 bonds) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (29.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-17.230
kcal/mol
LE
-0.479
kcal/mol/HA
Fit Quality
-4.86
FQ (Leeson)
HAC
36
heavy atoms
MW
526
Da
LogP
5.89
cLogP
Final rank
2.7730
rank score
Inter norm
-0.576
normalised
Contacts
13
H-bonds 7
Strain ΔE
29.3 kcal/mol
SASA buried
55%
Lipo contact
79% BSA apolar/total
SASA unbound
749 Ų
Apolar buried
329 Ų

Interaction summary

HBD 2 HBA 2 HY 3 PI 2 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
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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.40RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
518 1.5317635819657096 -0.88026 -24.6218 3 19 0 0.00 0.00 - no Open
453 1.7074599916409356 -0.665198 -16.9126 2 19 0 0.00 0.00 - no Open
539 2.7039259759344065 -0.701134 -19.8874 5 13 0 0.00 0.00 - no Open
440 2.732464516163644 -0.883815 -28.3394 6 23 0 0.00 0.00 - no Open
478 2.7730499915817934 -0.576088 -17.2298 7 13 6 0.75 1.00 - no Current
462 3.5890135434641097 -0.656405 -20.7614 4 14 0 0.00 0.00 - no Open
511 4.286679271760215 -0.659078 -20.8376 8 22 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 -17.230kcal/mol
Ligand efficiency (LE) -0.4786kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.864
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 526.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.89
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 23.15kcal/mol
Minimised FF energy -6.18kcal/mol

SASA & burial

✓ computed
SASA (unbound) 749.3Ų
Total solvent-accessible surface area of free ligand
BSA total 415.3Ų
Buried surface area upon binding
BSA apolar 328.7Ų
Hydrophobic contacts buried
BSA polar 86.7Ų
Polar contacts buried
Fraction buried 55.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3136.2Ų
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 1528.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)