FAIRMol

MK169

Pose ID 14468 Compound 2586 Pose 230

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
T22
L. donovani rab5a L. donovani
Ligand MK169

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
28.4 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.90, Jaccard 0.83, H-bond role recall 0.64
Burial
91%
Hydrophobic fit
73%
Reason: 9 internal clashes
9 intramolecular clashes 44% of hydrophobic surface appears solvent-exposed (7/16 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 (-1.108 kcal/mol/HA) ✓ Good fit quality (FQ -10.33) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (28.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.907
kcal/mol
LE
-1.108
kcal/mol/HA
Fit Quality
-10.33
FQ (Leeson)
HAC
27
heavy atoms
MW
413
Da
LogP
1.25
cLogP
Strain ΔE
28.4 kcal/mol
SASA buried
91%
Lipo contact
73% BSA apolar/total
SASA unbound
635 Ų
Apolar buried
421 Ų

Interaction summary

HB 12 HY 6 PI 1 CLASH 0 ⚠ Exposure 43%

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
No clash · clashes detected for this pose.
⚠️Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16 Buried (contacted) 9 Exposed 7 LogP 1.25 H-bonds 12
Exposed fragments: aliphatic chain/group (7 atoms exposed)
Final rank4.213Score-29.907
Inter norm-1.207Intra norm0.099
Top1000noExcludedno
Contacts21H-bonds12
Artifact reasongeometry warning; 9 clashes; 3 protein clashes; moderate strain Δ 27.9
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 ASP160 GLN42 GLU21 GLU73 GLY23 GLY25 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap19Native recall0.90
Jaccard0.83RMSD-
HB strict9Strict recall0.60
HB same residue+role7HB role recall0.64
HB same residue7HB residue recall0.64

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
250 1.848122234937569 -0.950603 -23.8357 4 18 0 0.00 0.00 - no Open
219 4.067117655395367 -1.06453 -27.7463 10 19 0 0.00 0.00 - no Open
230 4.213486809337062 -1.20677 -29.9075 12 21 19 0.90 0.64 - 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 -29.907kcal/mol
Ligand efficiency (LE) -1.1077kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.334
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 412.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.25
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 41.16kcal/mol
Minimised FF energy 12.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 634.9Ų
Total solvent-accessible surface area of free ligand
BSA total 575.3Ų
Buried surface area upon binding
BSA apolar 421.1Ų
Hydrophobic contacts buried
BSA polar 154.2Ų
Polar contacts buried
Fraction buried 90.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1353.1Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 490.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)