FAIRMol

MK213

Pose ID 6306 Compound 534 Pose 210

DB SELECTIONDocking 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 MK213

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
27.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.36
Burial
64%
Hydrophobic fit
80%
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 (-0.875 kcal/mol/HA) ✓ Good fit quality (FQ -8.44) ✓ Strong H-bond network (13 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (27.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-26.255
kcal/mol
LE
-0.875
kcal/mol/HA
Fit Quality
-8.44
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
27.8 kcal/mol
SASA buried
64%
Lipo contact
80% BSA apolar/total
SASA unbound
698 Ų
Apolar buried
354 Ų

Interaction summary

HB 13 HY 6 PI 2 CLASH 4 ⚠ Exposure 65%
🚨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 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank3.432Score-26.255
Inter norm-1.013Intra norm0.138
Top1000noExcludedno
Contacts17H-bonds13
Artifact reasongeometry warning; 12 clashes; 1 protein clash; moderate strain Δ 27.8
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49

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

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 overlap17Native recall1.00
Jaccard1.00RMSD-
HB strict5Strict recall0.38
HB same residue+role4HB role recall0.36
HB same residue6HB residue recall0.55

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

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 Current
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 Open
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 -26.255kcal/mol
Ligand efficiency (LE) -0.8752kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.442
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) 27.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 54.81kcal/mol
Minimised FF energy 27.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 698.5Ų
Total solvent-accessible surface area of free ligand
BSA total 443.3Ų
Buried surface area upon binding
BSA apolar 353.9Ų
Hydrophobic contacts buried
BSA polar 89.4Ų
Polar contacts buried
Fraction buried 63.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2330.2Ų
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 676.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)