FAIRMol

MK69

Pose ID 8315 Compound 3928 Pose 185

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand MK69
PDB1F3T↗

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
28.8 kcal/mol
Protein clashes
0
Internal clashes
6
Native overlap
contact recall 0.79, Jaccard 0.58, H-bond role recall 0.57
Burial
84%
Hydrophobic fit
71%
Reason: 6 internal clashes
6 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (10/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.018 kcal/mol/HA) ✓ Good fit quality (FQ -9.38) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (28.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-26.460
kcal/mol
LE
-1.018
kcal/mol/HA
Fit Quality
-9.38
FQ (Leeson)
HAC
26
heavy atoms
MW
397
Da
LogP
3.46
cLogP
Final rank
3.8393
rank score
Inter norm
-1.177
normalised
Contacts
22
H-bonds 13
Strain ΔE
28.8 kcal/mol
SASA buried
84%
Lipo contact
71% BSA apolar/total
SASA unbound
709 Ų
Apolar buried
422 Ų

Interaction summary

HBD 1 HBA 10 HY 3 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap15Native recall0.79
Jaccard0.58RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
185 3.839257507523653 -1.17679 -26.4602 13 22 15 0.79 0.57 - no Current
208 4.065129326390034 -1.11081 -23.3932 10 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 -26.460kcal/mol
Ligand efficiency (LE) -1.0177kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.376
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 396.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.46
Lipinski: ≤ 5
Rotatable bonds 14

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.58kcal/mol
Minimised FF energy 28.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 709.0Ų
Total solvent-accessible surface area of free ligand
BSA total 596.5Ų
Buried surface area upon binding
BSA apolar 421.6Ų
Hydrophobic contacts buried
BSA polar 175.0Ų
Polar contacts buried
Fraction buried 84.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2583.1Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1391.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)