FAIRMol

MK190

Pose ID 9873 Compound 72 Pose 387

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand MK190
PDB9IFF↗

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
21.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.69, Jaccard 0.41
Burial
74%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (12/25 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 (-0.451 kcal/mol/HA) ✓ Good fit quality (FQ -4.47) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (21.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-14.874
kcal/mol
LE
-0.451
kcal/mol/HA
Fit Quality
-4.47
FQ (Leeson)
HAC
33
heavy atoms
MW
520
Da
LogP
7.11
cLogP
Final rank
2.6314
rank score
Inter norm
-0.723
normalised
Contacts
18
H-bonds 3
Strain ΔE
21.6 kcal/mol
SASA buried
74%
Lipo contact
73% BSA apolar/total
SASA unbound
803 Ų
Apolar buried
438 Ų

Interaction summary

HBD 1 HY 8 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap9Native recall0.69
Jaccard0.41RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
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:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
331 0.8049376435843102 -0.802507 -28.4152 2 16 0 0.00 - - no Open
319 0.910123274535835 -0.816947 -25.8454 6 19 0 0.00 - - no Open
301 2.44839856690449 -0.740468 -23.9654 3 19 0 0.00 - - no Open
387 2.6313911897218505 -0.72292 -14.874 3 18 9 0.69 - - no Current
266 2.8065494362152568 -0.967782 -27.9485 4 22 0 0.00 - - no Open
320 2.934302685223078 -0.781101 -24.6404 2 19 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 -14.874kcal/mol
Ligand efficiency (LE) -0.4507kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 520.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 7.11
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 52.44kcal/mol
Minimised FF energy 30.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 803.0Ų
Total solvent-accessible surface area of free ligand
BSA total 596.9Ų
Buried surface area upon binding
BSA apolar 438.1Ų
Hydrophobic contacts buried
BSA polar 158.8Ų
Polar contacts buried
Fraction buried 74.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3026.5Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1556.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)