FAIRMol

Z49718975

Pose ID 8562 Compound 2096 Pose 432

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 Z49718975
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 medium Native strong SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.43
Burial
92%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.430 kcal/mol/HA) ✓ Good fit quality (FQ -11.46) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (18.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.733
kcal/mol
LE
-1.430
kcal/mol/HA
Fit Quality
-11.46
FQ (Leeson)
HAC
18
heavy atoms
MW
265
Da
LogP
1.99
cLogP
Final rank
1.5092
rank score
Inter norm
-1.600
normalised
Contacts
20
H-bonds 8
Strain ΔE
18.6 kcal/mol
SASA buried
92%
Lipo contact
75% BSA apolar/total
SASA unbound
466 Ų
Apolar buried
320 Ų

Interaction summary

HBD 2 HBA 5 PC 1 HY 4 PI 3 CLASH 3

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

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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
Jaccard0.62RMSD-
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
432 1.50916021506044 -1.60024 -25.7335 8 20 15 0.79 0.43 - no Current
405 1.7998442543703592 -2.02521 -38.4745 9 11 0 0.00 0.00 - no Open
527 2.5271626374165113 -1.36405 -20.2563 5 12 0 0.00 0.00 - no Open
431 3.2058566580264554 -1.55184 -28.9653 12 17 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -25.733kcal/mol
Ligand efficiency (LE) -1.4296kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.457
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 264.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.99
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 91.56kcal/mol
Minimised FF energy 72.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 465.9Ų
Total solvent-accessible surface area of free ligand
BSA total 428.5Ų
Buried surface area upon binding
BSA apolar 320.0Ų
Hydrophobic contacts buried
BSA polar 108.5Ų
Polar contacts buried
Fraction buried 92.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2433.1Ų
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 1378.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)