FAIRMol

KB_chagas_164

Pose ID 8985 Compound 3606 Pose 177

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand KB_chagas_164
PDB1NJJ↗

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 high Native mixed SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.32, H-bond role recall 0.20
Burial
84%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
2 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (8/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.807 kcal/mol/HA) ✓ Good fit quality (FQ -7.23) ✓ Good H-bonds (4 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Moderate strain (19.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-19.363
kcal/mol
LE
-0.807
kcal/mol/HA
Fit Quality
-7.23
FQ (Leeson)
HAC
24
heavy atoms
MW
337
Da
LogP
2.44
cLogP
Final rank
2.3027
rank score
Inter norm
-0.915
normalised
Contacts
18
H-bonds 6
Strain ΔE
19.0 kcal/mol
SASA buried
84%
Lipo contact
78% BSA apolar/total
SASA unbound
584 Ų
Apolar buried
382 Ų

Interaction summary

HBD 2 HBA 2 HY 2 PI 0 CLASH 2

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap8Native recall0.53
Jaccard0.32RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
144 0.5290015110922954 -1.0613 -21.5743 3 11 0 0.00 0.00 - no Open
177 2.302710783536821 -0.915306 -19.3633 6 18 8 0.53 0.20 - 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 -19.363kcal/mol
Ligand efficiency (LE) -0.8068kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.231
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.44
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -213.25kcal/mol
Minimised FF energy -232.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 583.9Ų
Total solvent-accessible surface area of free ligand
BSA total 490.6Ų
Buried surface area upon binding
BSA apolar 382.2Ų
Hydrophobic contacts buried
BSA polar 108.4Ų
Polar contacts buried
Fraction buried 84.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2427.8Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1382.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)