FAIRMol

MK220

Pose ID 11811 Compound 2157 Pose 290

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 MK220
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
23.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.77, Jaccard 0.50
Burial
69%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.451 kcal/mol/HA) ✓ Good fit quality (FQ -4.44) ✓ Good H-bonds (4 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ High strain energy (23.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-14.433
kcal/mol
LE
-0.451
kcal/mol/HA
Fit Quality
-4.44
FQ (Leeson)
HAC
32
heavy atoms
MW
438
Da
LogP
4.28
cLogP
Final rank
3.8782
rank score
Inter norm
-0.733
normalised
Contacts
17
H-bonds 9
Strain ΔE
23.7 kcal/mol
SASA buried
69%
Lipo contact
84% BSA apolar/total
SASA unbound
720 Ų
Apolar buried
417 Ų

Interaction summary

HBD 1 HBA 3 HY 7 PI 2 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
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.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap10Native recall0.77
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
274 0.5742700777155489 -0.990165 -27.1203 8 12 0 0.00 - - no Open
261 0.9719492413306788 -0.779872 -18.5123 6 19 0 0.00 - - no Open
250 2.2553998643367166 -0.8863 -22.4828 4 14 0 0.00 - - no Open
238 2.890295633710476 -0.925711 -29.2458 13 20 0 0.00 - - no Open
290 3.8782243837340302 -0.732874 -14.4334 9 17 10 0.77 - - 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 -14.433kcal/mol
Ligand efficiency (LE) -0.4510kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.436
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.28
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 51.48kcal/mol
Minimised FF energy 27.83kcal/mol

SASA & burial

✓ computed
SASA (unbound) 719.6Ų
Total solvent-accessible surface area of free ligand
BSA total 497.8Ų
Buried surface area upon binding
BSA apolar 416.6Ų
Hydrophobic contacts buried
BSA polar 81.2Ų
Polar contacts buried
Fraction buried 69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3263.3Ų
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 1446.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)