FAIRMol

Z275024592

Pose ID 8491 Compound 2284 Pose 361

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 Z275024592
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
14.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.71
Burial
76%
Hydrophobic fit
60%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.965 kcal/mol/HA) ✓ Good fit quality (FQ -9.31) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (60%) ✗ Moderate strain (14.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-28.945
kcal/mol
LE
-0.965
kcal/mol/HA
Fit Quality
-9.31
FQ (Leeson)
HAC
30
heavy atoms
MW
451
Da
LogP
4.71
cLogP
Final rank
2.8436
rank score
Inter norm
-0.924
normalised
Contacts
16
H-bonds 10
Strain ΔE
14.7 kcal/mol
SASA buried
76%
Lipo contact
60% BSA apolar/total
SASA unbound
673 Ų
Apolar buried
308 Ų

Interaction summary

HBD 1 HBA 6 HY 5 PI 3 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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: permissive.
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 overlap13Native recall0.68
Jaccard0.59RMSD-
HB strict6Strict recall0.67
HB same residue+role5HB role recall0.71
HB same residue5HB residue recall0.71

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
343 -0.016781169744085098 -1.00863 -28.5549 5 14 0 0.00 0.00 - no Open
361 0.39586097939460907 -0.943264 -20.6961 1 18 0 0.00 0.00 - no Open
464 1.4734933962778927 -0.826777 -25.3273 3 18 1 0.05 0.00 - no Open
326 1.5781974143203685 -1.09282 -32.0683 3 22 0 0.00 0.00 - no Open
389 1.943848181712128 -0.926403 -25.5192 7 17 0 0.00 0.00 - no Open
361 2.8436288692052334 -0.924051 -28.9454 10 16 13 0.68 0.71 - no Current
364 3.019765575265047 -0.826602 -24.7265 5 12 0 0.00 0.00 - no Open
356 3.4461648256018282 -0.916897 -26.8047 7 18 0 0.00 0.00 - no Open
386 3.5274002705054572 -0.814362 -24.8371 7 11 0 0.00 0.00 - no Open
363 3.5536977263405602 -1.05422 -31.1436 10 19 0 0.00 0.00 - no Open
402 3.832040767874197 -0.721821 -22.5586 9 12 0 0.00 0.00 - no Open
330 3.8955722111935605 -0.975688 -30.3598 6 14 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 -28.945kcal/mol
Ligand efficiency (LE) -0.9648kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.307
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 450.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.71
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 24.18kcal/mol
Minimised FF energy 9.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 673.2Ų
Total solvent-accessible surface area of free ligand
BSA total 511.3Ų
Buried surface area upon binding
BSA apolar 307.6Ų
Hydrophobic contacts buried
BSA polar 203.7Ų
Polar contacts buried
Fraction buried 75.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 60.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2504.0Ų
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 1411.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)