FAIRMol

KB_chagas_97

Pose ID 8237 Compound 4000 Pose 107

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_chagas_97
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.74, Jaccard 0.52, H-bond role recall 0.29
Burial
83%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.935 kcal/mol/HA) ✓ Good fit quality (FQ -8.83) ✓ Good H-bonds (3 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Moderate strain (19.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-26.189
kcal/mol
LE
-0.935
kcal/mol/HA
Fit Quality
-8.83
FQ (Leeson)
HAC
28
heavy atoms
MW
412
Da
LogP
3.53
cLogP
Final rank
2.9161
rank score
Inter norm
-0.987
normalised
Contacts
22
H-bonds 9
Strain ΔE
19.0 kcal/mol
SASA buried
83%
Lipo contact
78% BSA apolar/total
SASA unbound
673 Ų
Apolar buried
433 Ų

Interaction summary

HBD 2 HBA 1 HY 2 PI 3 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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.
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 overlap14Native recall0.74
Jaccard0.52RMSD-
HB strict2Strict recall0.22
HB same residue+role2HB role recall0.29
HB same residue2HB residue recall0.29

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
172 1.9134998045254397 -0.79303 -20.8753 6 16 0 0.00 0.00 - no Open
181 2.8366532868781027 -0.68708 -18.3087 7 12 0 0.00 0.00 - no Open
107 2.9160797128979166 -0.986747 -26.1895 9 22 14 0.74 0.29 - no Current
126 4.1586623052380025 -0.847622 -21.9701 4 15 0 0.00 0.00 - no Open
107 4.636484064309373 -1.23657 -34.0694 11 22 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 -26.189kcal/mol
Ligand efficiency (LE) -0.9353kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.830
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 411.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.53
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 66.46kcal/mol
Minimised FF energy 47.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 673.0Ų
Total solvent-accessible surface area of free ligand
BSA total 556.9Ų
Buried surface area upon binding
BSA apolar 432.7Ų
Hydrophobic contacts buried
BSA polar 124.2Ų
Polar contacts buried
Fraction buried 82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2592.3Ų
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 1375.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)