FAIRMol

KB_Leish_139

Pose ID 8224 Compound 3144 Pose 94

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 KB_Leish_139
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
42.8 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.57
Burial
69%
Hydrophobic fit
70%
Reason: 10 internal clashes, strain 42.8 kcal/mol
strain ΔE 42.8 kcal/mol 10 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.630 kcal/mol/HA) ✓ Good fit quality (FQ -6.25) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Extreme strain energy (42.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-20.788
kcal/mol
LE
-0.630
kcal/mol/HA
Fit Quality
-6.25
FQ (Leeson)
HAC
33
heavy atoms
MW
486
Da
LogP
4.13
cLogP
Strain ΔE
42.8 kcal/mol
SASA buried
69%
Lipo contact
70% BSA apolar/total
SASA unbound
766 Ų
Apolar buried
370 Ų

Interaction summary

HB 7 HY 10 PI 2 CLASH 0

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
No clash · clashes detected for this pose.
Final rank4.678Score-20.788
Inter norm-0.844Intra norm0.215
Top1000noExcludedno
Contacts18H-bonds7
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; high strain Δ 42.8
Residues
ALA67 ALA90 ARG154 ARG277 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS169 LYS69 PHE170 PHE238 PRO275 SER200 TYR278 TYR389

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
Jaccard0.68RMSD-
HB strict4Strict recall0.44
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
159 2.7905803072646633 -0.972055 -21.8074 6 19 0 0.00 0.00 - no Open
165 3.4814291767636494 -0.588155 -12.3932 6 10 0 0.00 0.00 - no Open
94 4.678355134459097 -0.844499 -20.7875 7 18 15 0.79 0.57 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -20.788kcal/mol
Ligand efficiency (LE) -0.6299kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.250
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 485.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.13
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 42.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 75.93kcal/mol
Minimised FF energy 33.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 766.0Ų
Total solvent-accessible surface area of free ligand
BSA total 525.7Ų
Buried surface area upon binding
BSA apolar 370.1Ų
Hydrophobic contacts buried
BSA polar 155.6Ų
Polar contacts buried
Fraction buried 68.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2637.5Ų
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 1415.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)