FAIRMol

Z198115550

Pose ID 8623 Compound 4006 Pose 493

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 Z198115550
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 high Native strong SASA done
Strain ΔE
8.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.79, H-bond role recall 0.43
Burial
90%
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
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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.963 kcal/mol/HA) ✓ Good fit quality (FQ -14.04) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (8.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-27.484
kcal/mol
LE
-1.963
kcal/mol/HA
Fit Quality
-14.04
FQ (Leeson)
HAC
14
heavy atoms
MW
212
Da
LogP
0.69
cLogP
Final rank
3.0933
rank score
Inter norm
-2.028
normalised
Contacts
15
H-bonds 7
Strain ΔE
8.6 kcal/mol
SASA buried
90%
Lipo contact
70% BSA apolar/total
SASA unbound
400 Ų
Apolar buried
254 Ų

Interaction summary

HBD 2 HBA 5 HY 3 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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 overlap15Native recall0.79
Jaccard0.79RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
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
493 3.093321768743285 -2.0282 -27.4836 7 15 15 0.79 0.43 - 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 -27.484kcal/mol
Ligand efficiency (LE) -1.9631kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.037
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 212.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.69
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 8.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -71.65kcal/mol
Minimised FF energy -80.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 400.5Ų
Total solvent-accessible surface area of free ligand
BSA total 361.7Ų
Buried surface area upon binding
BSA apolar 254.1Ų
Hydrophobic contacts buried
BSA polar 107.6Ų
Polar contacts buried
Fraction buried 90.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2376.2Ų
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 1377.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)