FAIRMol

KB_HAT_192

Pose ID 8212 Compound 4058 Pose 82

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_HAT_192
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
89.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.47, H-bond role recall 0.29
Burial
82%
Hydrophobic fit
83%
Reason: strain 89.1 kcal/mol
strain ΔE 89.1 kcal/mol 2 protein-contact clashes 39% of hydrophobic surface appears solvent-exposed (9/23 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
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.674 kcal/mol/HA) ✓ Good fit quality (FQ -6.69) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (89.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-22.252
kcal/mol
LE
-0.674
kcal/mol/HA
Fit Quality
-6.69
FQ (Leeson)
HAC
33
heavy atoms
MW
468
Da
LogP
1.62
cLogP
Final rank
4.7090
rank score
Inter norm
-0.914
normalised
Contacts
25
H-bonds 11
Strain ΔE
89.1 kcal/mol
SASA buried
82%
Lipo contact
83% BSA apolar/total
SASA unbound
794 Ų
Apolar buried
538 Ų

Interaction summary

HBD 1 HBA 6 HY 6 PI 2 CLASH 2

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
Jaccard0.47RMSD-
HB strict4Strict recall0.44
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
82 4.708980444102277 -0.913578 -22.2521 11 25 14 0.74 0.29 - 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 -22.252kcal/mol
Ligand efficiency (LE) -0.6743kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.690
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 467.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.62
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 89.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 107.91kcal/mol
Minimised FF energy 18.85kcal/mol

SASA & burial

✓ computed
SASA (unbound) 794.0Ų
Total solvent-accessible surface area of free ligand
BSA total 651.6Ų
Buried surface area upon binding
BSA apolar 538.4Ų
Hydrophobic contacts buried
BSA polar 113.2Ų
Polar contacts buried
Fraction buried 82.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2722.4Ų
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 1417.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)