FAIRMol

MK4

Pose ID 11120 Compound 3955 Pose 277

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand MK4
PDB5S9T↗

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 mixed SASA done
Strain ΔE
20.4 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.50, Jaccard 0.24, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
79%
Reason: 18 internal clashes
18 intramolecular clashes
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 High Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.733 kcal/mol/HA) ✓ Good fit quality (FQ -7.39) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (20.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-25.655
kcal/mol
LE
-0.733
kcal/mol/HA
Fit Quality
-7.39
FQ (Leeson)
HAC
35
heavy atoms
MW
481
Da
LogP
3.20
cLogP
Final rank
4.3295
rank score
Inter norm
-0.715
normalised
Contacts
19
H-bonds 6
Strain ΔE
20.4 kcal/mol
SASA buried
80%
Lipo contact
79% BSA apolar/total
SASA unbound
779 Ų
Apolar buried
493 Ų

Interaction summary

HBD 3 HBA 2 HY 8 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap6Native recall0.50
Jaccard0.24RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
375 3.355204376370653 -0.739531 -20.079 7 14 0 0.00 0.00 - no Open
277 4.329492327669684 -0.714893 -25.655 6 19 6 0.50 0.00 - no Current
197 4.9367112996547835 -0.819354 -22.3352 8 17 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 -25.655kcal/mol
Ligand efficiency (LE) -0.7330kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.393
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 480.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.20
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.43kcal/mol
Minimised FF energy 70.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 778.8Ų
Total solvent-accessible surface area of free ligand
BSA total 622.6Ų
Buried surface area upon binding
BSA apolar 493.3Ų
Hydrophobic contacts buried
BSA polar 129.3Ų
Polar contacts buried
Fraction buried 79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6649.2Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2056.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)