FAIRMol

Z29884022

Pose ID 11978 Compound 1766 Pose 457

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z29884022
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
17.1 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.62, Jaccard 0.50
Burial
66%
Hydrophobic fit
83%
Reason: 10 internal clashes
10 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.694 kcal/mol/HA) ✓ Good fit quality (FQ -6.31) ✓ Good H-bonds (5 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (17.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-17.346
kcal/mol
LE
-0.694
kcal/mol/HA
Fit Quality
-6.31
FQ (Leeson)
HAC
25
heavy atoms
MW
337
Da
LogP
3.24
cLogP
Strain ΔE
17.1 kcal/mol
SASA buried
66%
Lipo contact
83% BSA apolar/total
SASA unbound
601 Ų
Apolar buried
331 Ų

Interaction summary

HB 5 HY 19 PI 2 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank3.111Score-17.346
Inter norm-0.827Intra norm0.133
Top1000noExcludedno
Contacts11H-bonds5
Artifact reasongeometry warning; 10 clashes; 2 protein clashes
Residues
CYS52 GLU18 ILE339 LEU17 MET113 SER14 THR335 TRP21 TYR110 VAL53 VAL58

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap8Native recall0.62
Jaccard0.50RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
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:276; 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
415 0.6019940514467164 -0.909601 -20.1474 0 17 0 0.00 - - no Open
428 1.154995800561394 -1.18339 -26.1237 2 11 0 0.00 - - no Open
457 3.1110710607896723 -0.826808 -17.3463 5 11 8 0.62 - - 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 -17.346kcal/mol
Ligand efficiency (LE) -0.6939kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.308
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.24
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 74.42kcal/mol
Minimised FF energy 57.35kcal/mol

SASA & burial

✓ computed
SASA (unbound) 600.5Ų
Total solvent-accessible surface area of free ligand
BSA total 396.7Ų
Buried surface area upon binding
BSA apolar 330.9Ų
Hydrophobic contacts buried
BSA polar 65.8Ų
Polar contacts buried
Fraction buried 66.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3118.3Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1481.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)