FAIRMol

Z44868759

Pose ID 11934 Compound 3798 Pose 413

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z44868759
PDB6RB5↗

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 mixed SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.37
Burial
73%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.222 kcal/mol/HA) ✓ Good fit quality (FQ -10.23) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Moderate strain (15.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-24.445
kcal/mol
LE
-1.222
kcal/mol/HA
Fit Quality
-10.23
FQ (Leeson)
HAC
20
heavy atoms
MW
331
Da
LogP
3.48
cLogP
Strain ΔE
15.9 kcal/mol
SASA buried
73%
Lipo contact
79% BSA apolar/total
SASA unbound
491 Ų
Apolar buried
284 Ų

Interaction summary

HB 7 HY 18 PI 2 CLASH 1

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
Final rank2.741Score-24.445
Inter norm-1.204Intra norm-0.018
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 7 clashes; 2 protein clashes
Residues
CYS52 GLU18 GLY13 GLY49 GLY50 ILE339 LEU17 MET113 SER14 THR335 TRP21 TYR110 VAL53

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 overlap7Native recall0.54
Jaccard0.37RMSD-
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
413 2.7409533676114433 -1.20449 -24.4445 7 13 7 0.54 - - no Current
389 3.4434232084832646 -1.10295 -21.9006 6 11 0 0.00 - - no Open
373 3.634073454356905 -1.21205 -25.5922 6 12 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 -24.445kcal/mol
Ligand efficiency (LE) -1.2222kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.228
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 331.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.48
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 60.31kcal/mol
Minimised FF energy 44.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 491.1Ų
Total solvent-accessible surface area of free ligand
BSA total 358.6Ų
Buried surface area upon binding
BSA apolar 284.2Ų
Hydrophobic contacts buried
BSA polar 74.4Ų
Polar contacts buried
Fraction buried 73.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2978.3Ų
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 1515.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)