FAIRMol

Z56920485

Pose ID 8741 Compound 3978 Pose 611

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 Z56920485
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 medium Native strong SASA done
Strain ΔE
39.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.64, H-bond role recall 0.43
Burial
77%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
1 protein-contact clashes 59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.152 kcal/mol/HA) ✓ Good fit quality (FQ -10.33) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (39.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-27.656
kcal/mol
LE
-1.152
kcal/mol/HA
Fit Quality
-10.33
FQ (Leeson)
HAC
24
heavy atoms
MW
347
Da
LogP
3.09
cLogP
Final rank
1.9978
rank score
Inter norm
-1.329
normalised
Contacts
17
H-bonds 8
Strain ΔE
39.8 kcal/mol
SASA buried
77%
Lipo contact
77% BSA apolar/total
SASA unbound
585 Ų
Apolar buried
347 Ų

Interaction summary

HBD 3 HBA 5 HY 2 PI 2 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 overlap14Native recall0.74
Jaccard0.64RMSD-
HB strict4Strict recall0.44
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
611 1.9977621387273847 -1.329 -27.6558 8 17 14 0.74 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 -27.656kcal/mol
Ligand efficiency (LE) -1.1523kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.327
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.09
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 95.77kcal/mol
Minimised FF energy 56.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 585.0Ų
Total solvent-accessible surface area of free ligand
BSA total 451.1Ų
Buried surface area upon binding
BSA apolar 347.3Ų
Hydrophobic contacts buried
BSA polar 103.8Ų
Polar contacts buried
Fraction buried 77.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2527.2Ų
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 1375.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)