FAIRMol

KB_chagas_101

Pose ID 8238 Compound 4016 Pose 108

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 KB_chagas_101
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
12.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.57
Burial
77%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes
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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.061 kcal/mol/HA) ✓ Good fit quality (FQ -10.13) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (12.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-30.774
kcal/mol
LE
-1.061
kcal/mol/HA
Fit Quality
-10.13
FQ (Leeson)
HAC
29
heavy atoms
MW
389
Da
LogP
2.27
cLogP
Final rank
3.3922
rank score
Inter norm
-0.987
normalised
Contacts
16
H-bonds 12
Strain ΔE
12.1 kcal/mol
SASA buried
77%
Lipo contact
70% BSA apolar/total
SASA unbound
618 Ų
Apolar buried
332 Ų

Interaction summary

HBA 11 HY 3 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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: permissive.
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 overlap12Native recall0.63
Jaccard0.52RMSD-
HB strict6Strict recall0.67
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
108 3.39219694684085 -0.986512 -30.7739 12 16 12 0.63 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 -30.774kcal/mol
Ligand efficiency (LE) -1.0612kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.130
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 389.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 23.10kcal/mol
Minimised FF energy 10.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 617.9Ų
Total solvent-accessible surface area of free ligand
BSA total 473.1Ų
Buried surface area upon binding
BSA apolar 332.4Ų
Hydrophobic contacts buried
BSA polar 140.8Ų
Polar contacts buried
Fraction buried 76.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2549.7Ų
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 1383.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)