FAIRMol

MK216

Pose ID 6309 Compound 534 Pose 213

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 MK216

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
16.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.36
Burial
63%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (15/23 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 (-0.944 kcal/mol/HA) ✓ Good fit quality (FQ -9.10) ✓ Strong H-bond network (11 bonds) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (16.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-28.305
kcal/mol
LE
-0.944
kcal/mol/HA
Fit Quality
-9.10
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
16.7 kcal/mol
SASA buried
63%
Lipo contact
77% BSA apolar/total
SASA unbound
703 Ų
Apolar buried
339 Ų

Interaction summary

HB 11 HY 1 PI 2 CLASH 4 ⚠ Exposure 65%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (15/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 23 Buried (contacted) 8 Exposed 15 LogP 3.8 H-bonds 11
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank4.298Score-28.305
Inter norm-1.000Intra norm0.056
Top1000noExcludedno
Contacts16H-bonds11
Artifact reasongeometry warning; 12 clashes; 2 protein clashes
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 SER46 THR74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap15Native recall0.88
Jaccard0.83RMSD-
HB strict5Strict recall0.38
HB same residue+role4HB role recall0.36
HB same residue5HB residue recall0.45

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
263 1.0267699428225585 -1.16463 -31.7677 11 13 0 0.00 0.00 - no Open
248 1.0565759821753493 -1.05865 -27.2137 11 11 0 0.00 0.00 - no Open
275 1.158072578337196 -0.79049 -20.4723 4 16 0 0.00 0.00 - no Open
326 1.522628122716502 -0.968338 -25.9969 6 13 0 0.00 0.00 - no Open
244 1.708744967754064 -0.825708 -20.6159 5 19 0 0.00 0.00 - no Open
257 1.8345663825114074 -0.798505 -19.855 3 19 0 0.00 0.00 - no Open
309 1.905113599274035 -0.859805 -26.3343 3 12 0 0.00 0.00 - no Open
209 2.4824832058938013 -1.05337 -29.243 13 18 5 0.29 0.27 - no Open
204 2.663282674439042 -1.13906 -30.5138 11 18 0 0.00 0.00 - no Open
270 2.7066301048038337 -0.90359 -23.3047 8 16 0 0.00 0.00 - no Open
335 3.062936325722447 -0.858552 -27.4791 7 19 0 0.00 0.00 - no Open
224 3.0864929722424383 -0.941482 -26.4284 4 18 0 0.00 0.00 - no Open
308 3.1241016565923485 -1.04343 -27.852 6 10 0 0.00 0.00 - no Open
210 3.431812628247348 -1.01323 -26.2551 13 17 17 1.00 0.36 - no Open
200 4.283886601626247 -0.994469 -27.0487 13 17 17 1.00 0.36 - no Open
213 4.298392329825456 -0.999515 -28.3054 11 16 15 0.88 0.36 - no Current
307 4.451695165235262 -0.776336 -19.1475 5 13 0 0.00 0.00 - no Open
249 5.404412263953654 -0.824137 -19.6852 7 12 0 0.00 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 -28.305kcal/mol
Ligand efficiency (LE) -0.9435kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.101
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.32kcal/mol
Minimised FF energy 36.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 702.7Ų
Total solvent-accessible surface area of free ligand
BSA total 440.6Ų
Buried surface area upon binding
BSA apolar 338.9Ų
Hydrophobic contacts buried
BSA polar 101.8Ų
Polar contacts buried
Fraction buried 62.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2328.9Ų
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 677.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)