FAIRMol

MK218

Pose ID 6311 Compound 739 Pose 215

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
T10
L. infantum R5P L. infantum
Ligand MK218

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
19.6 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 1.00, Jaccard 0.94, H-bond role recall 0.45
Burial
61%
Hydrophobic fit
76%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (16/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.932 kcal/mol/HA) ✓ Good fit quality (FQ -9.08) ✓ Strong H-bond network (7 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (19.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-28.885
kcal/mol
LE
-0.932
kcal/mol/HA
Fit Quality
-9.08
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.89
cLogP
Final rank
4.2739
rank score
Inter norm
-1.011
normalised
Contacts
18
H-bonds 9
Strain ΔE
19.6 kcal/mol
SASA buried
61%
Lipo contact
76% BSA apolar/total
SASA unbound
724 Ų
Apolar buried
334 Ų

Interaction summary

HBD 2 HBA 5 HY 2 PI 2 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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: permissive.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap17Native recall1.00
Jaccard0.94RMSD-
HB strict5Strict recall0.38
HB same residue+role5HB role recall0.45
HB same residue7HB residue recall0.64

Protein summary

155 residues
Protein targetT10Atoms4590
Residues155Chains1
Residue summaryILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
272 0.36726388649663205 -1.07634 -28.4462 9 16 0 0.00 0.00 - no Open
329 1.0999927831279912 -0.892143 -20.6112 3 19 0 0.00 0.00 - no Open
247 1.8367897261852835 -0.996002 -28.4151 5 17 0 0.00 0.00 - no Open
328 2.868228427114262 -0.971001 -29.1342 5 15 0 0.00 0.00 - no Open
209 3.202189693744015 -0.93039 -24.7522 7 15 0 0.00 0.00 - no Open
239 3.3044571743805284 -1.13103 -27.1386 13 24 0 0.00 0.00 - no Open
236 3.688372365417219 -0.891707 -23.7953 8 18 5 0.29 0.18 - no Open
215 4.273909764805231 -1.01116 -28.8847 9 18 17 1.00 0.45 - 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 -28.885kcal/mol
Ligand efficiency (LE) -0.9318kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.89
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 51.78kcal/mol
Minimised FF energy 32.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 724.2Ų
Total solvent-accessible surface area of free ligand
BSA total 441.6Ų
Buried surface area upon binding
BSA apolar 334.3Ų
Hydrophobic contacts buried
BSA polar 107.2Ų
Polar contacts buried
Fraction buried 61.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2354.3Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 669.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)