FAIRMol

MK15

Pose ID 8306 Compound 447 Pose 176

DB SELECTIONDocking 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 MK15
PDB1F3T↗

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
47.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.67, H-bond role recall 0.43
Burial
76%
Hydrophobic fit
82%
Reason: strain 47.7 kcal/mol
strain ΔE 47.7 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.623 kcal/mol/HA) ✓ Good fit quality (FQ -6.42) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Extreme strain energy (47.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-23.657
kcal/mol
LE
-0.623
kcal/mol/HA
Fit Quality
-6.42
FQ (Leeson)
HAC
38
heavy atoms
MW
525
Da
LogP
1.37
cLogP
Strain ΔE
47.7 kcal/mol
SASA buried
76%
Lipo contact
82% BSA apolar/total
SASA unbound
795 Ų
Apolar buried
495 Ų

Interaction summary

HB 7 HY 22 PI 2 CLASH 3
Final rank3.303Score-23.657
Inter norm-0.778Intra norm0.155
Top1000noExcludedno
Contacts21H-bonds7
Artifact reasongeometry warning; 17 clashes; 1 protein clash; high strain Δ 36.8
Residues
ALA67 ARG154 ARG277 ASN327 ASP332 CYS328 GLU274 GLY236 GLY237 GLY276 GLY393 HIS197 LYS69 PHE170 PHE238 PRO275 SER200 TYR278 TYR331 TYR389 VAL392

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

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 overlap16Native recall0.84
Jaccard0.67RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
316 2.5967959105256178 -0.823231 -27.406 7 22 0 0.00 0.00 - no Open
176 3.302825141914426 -0.77766 -23.657 7 21 16 0.84 0.43 - no Current
298 4.66109913972578 -0.782625 -21.0419 6 24 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 -23.657kcal/mol
Ligand efficiency (LE) -0.6226kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.418
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 524.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.37
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 47.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 137.25kcal/mol
Minimised FF energy 89.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 795.1Ų
Total solvent-accessible surface area of free ligand
BSA total 606.3Ų
Buried surface area upon binding
BSA apolar 494.5Ų
Hydrophobic contacts buried
BSA polar 111.8Ų
Polar contacts buried
Fraction buried 76.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2753.3Ų
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 1365.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)