FAIRMol

Z49995281

Pose ID 8618 Compound 2861 Pose 488

DB SELECTIONDocking 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 Z49995281
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
28.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.57
Burial
73%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (9/16 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 (-1.006 kcal/mol/HA) ✓ Good fit quality (FQ -9.15) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (28.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-25.163
kcal/mol
LE
-1.006
kcal/mol/HA
Fit Quality
-9.15
FQ (Leeson)
HAC
25
heavy atoms
MW
364
Da
LogP
1.97
cLogP
Final rank
4.1265
rank score
Inter norm
-1.109
normalised
Contacts
18
H-bonds 12
Strain ΔE
28.1 kcal/mol
SASA buried
73%
Lipo contact
70% BSA apolar/total
SASA unbound
614 Ų
Apolar buried
314 Ų

Interaction summary

HBD 3 HBA 7 HY 2 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 8.

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
Jaccard0.68RMSD-
HB strict5Strict recall0.56
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
465 1.5974050306592176 -1.23716 -31.8258 8 15 0 0.00 0.00 - no Open
491 2.0187936003951927 -0.873159 -20.7678 5 17 0 0.00 0.00 - no Open
475 3.236351828504575 -1.08668 -25.6632 14 16 0 0.00 0.00 - no Open
488 4.126481732356995 -1.10914 -25.1633 12 18 15 0.79 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 -25.163kcal/mol
Ligand efficiency (LE) -1.0065kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.150
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 364.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.97
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 8.75kcal/mol
Minimised FF energy -19.39kcal/mol

SASA & burial

✓ computed
SASA (unbound) 614.0Ų
Total solvent-accessible surface area of free ligand
BSA total 450.1Ų
Buried surface area upon binding
BSA apolar 314.2Ų
Hydrophobic contacts buried
BSA polar 135.8Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2528.5Ų
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 1391.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)