FAIRMol

MK20

Pose ID 7652 Compound 3909 Pose 200

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 MK20
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.94, Jaccard 0.83, H-bond role recall 0.60
Burial
63%
Hydrophobic fit
83%
Reason: strain 43.3 kcal/mol
strain ΔE 43.3 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 74% of hydrophobic surface is solvent-exposed (20/27 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.693 kcal/mol/HA) ✓ Good fit quality (FQ -6.99) ✓ Strong H-bond network (11 bonds) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (43.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-24.256
kcal/mol
LE
-0.693
kcal/mol/HA
Fit Quality
-6.99
FQ (Leeson)
HAC
35
heavy atoms
MW
503
Da
LogP
2.69
cLogP
Final rank
3.6638
rank score
Inter norm
-0.851
normalised
Contacts
17
H-bonds 13
Strain ΔE
43.3 kcal/mol
SASA buried
63%
Lipo contact
83% BSA apolar/total
SASA unbound
809 Ų
Apolar buried
424 Ų

Interaction summary

HBD 1 HBA 10 HY 3 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 8.

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: 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
Jaccard0.83RMSD-
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
270 2.01712149113418 -0.652871 -18.7215 6 14 0 0.00 0.00 - no Open
200 3.663818620646783 -0.851327 -24.2562 13 17 15 0.94 0.60 - no Current
350 3.7647208863229964 -0.667122 -22.318 3 16 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 -24.256kcal/mol
Ligand efficiency (LE) -0.6930kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.990
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 502.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.69
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 133.14kcal/mol
Minimised FF energy 89.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 808.6Ų
Total solvent-accessible surface area of free ligand
BSA total 510.7Ų
Buried surface area upon binding
BSA apolar 423.8Ų
Hydrophobic contacts buried
BSA polar 86.9Ų
Polar contacts buried
Fraction buried 63.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2388.9Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 782.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)