FAIRMol

MK169

Pose ID 7671 Compound 2586 Pose 219

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
T12
T. brucei R5P T. brucei
Ligand MK169
PDB6FXS↗

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
21.4 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.94, Jaccard 0.75, H-bond role recall 0.60
Burial
82%
Hydrophobic fit
66%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (6/16 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 (-1.028 kcal/mol/HA) ✓ Good fit quality (FQ -9.59) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ High strain energy (21.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-27.746
kcal/mol
LE
-1.028
kcal/mol/HA
Fit Quality
-9.59
FQ (Leeson)
HAC
27
heavy atoms
MW
413
Da
LogP
1.25
cLogP
Strain ΔE
21.4 kcal/mol
SASA buried
82%
Lipo contact
66% BSA apolar/total
SASA unbound
663 Ų
Apolar buried
360 Ų

Interaction summary

HB 10 HY 13 PI 2 CLASH 6 ⚠ Exposure 37%

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
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16 Buried (contacted) 10 Exposed 6 LogP 1.25 H-bonds 10
Exposed fragments: aliphatic chain/group (6 atoms exposed)
Final rank4.067Score-27.746
Inter norm-1.065Intra norm0.037
Top1000noExcludedno
Contacts19H-bonds10
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; moderate strain Δ 21.4
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 MET78 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap15Native recall0.94
Jaccard0.75RMSD-
HB strict6Strict recall0.50
HB same residue+role6HB role recall0.60
HB same residue6HB residue recall0.60

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:CSD72

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 15 0.94 0.60 - no Current
230 4.213486809337062 -1.20677 -29.9075 12 21 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 -27.746kcal/mol
Ligand efficiency (LE) -1.0276kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.588
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) 21.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 37.64kcal/mol
Minimised FF energy 16.23kcal/mol

SASA & burial

✓ computed
SASA (unbound) 662.7Ų
Total solvent-accessible surface area of free ligand
BSA total 544.2Ų
Buried surface area upon binding
BSA apolar 360.1Ų
Hydrophobic contacts buried
BSA polar 184.1Ų
Polar contacts buried
Fraction buried 82.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2155.7Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 760.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)