FAIRMol

Z45537933

Pose ID 8604 Compound 3511 Pose 474

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 Z45537933
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
16.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.62, H-bond role recall 0.43
Burial
94%
Hydrophobic fit
68%
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 (-1.587 kcal/mol/HA) ✓ Good fit quality (FQ -13.54) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (16.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-33.326
kcal/mol
LE
-1.587
kcal/mol/HA
Fit Quality
-13.54
FQ (Leeson)
HAC
21
heavy atoms
MW
326
Da
LogP
0.81
cLogP
Final rank
4.0039
rank score
Inter norm
-1.661
normalised
Contacts
23
H-bonds 9
Strain ΔE
16.8 kcal/mol
SASA buried
94%
Lipo contact
68% BSA apolar/total
SASA unbound
548 Ų
Apolar buried
349 Ų

Interaction summary

HBD 1 HBA 7 HY 4 PI 2 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.

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 overlap16Native recall0.84
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
508 2.009788458540564 -1.01822 -20.5996 7 15 0 0.00 0.00 - no Open
545 3.4732770804134097 -1.18527 -23.981 4 15 0 0.00 0.00 - no Open
466 3.510541205591343 -1.43344 -28.2186 11 17 0 0.00 0.00 - no Open
482 3.5921666043258553 -1.53996 -31.7883 11 18 0 0.00 0.00 - no Open
469 3.966350797122376 -1.20182 -23.6843 13 15 0 0.00 0.00 - no Open
474 4.003880070761457 -1.66085 -33.326 9 23 16 0.84 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 -33.326kcal/mol
Ligand efficiency (LE) -1.5870kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.536
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.81
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -155.87kcal/mol
Minimised FF energy -172.71kcal/mol

SASA & burial

✓ computed
SASA (unbound) 547.9Ų
Total solvent-accessible surface area of free ligand
BSA total 513.1Ų
Buried surface area upon binding
BSA apolar 349.0Ų
Hydrophobic contacts buried
BSA polar 164.2Ų
Polar contacts buried
Fraction buried 93.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2456.0Ų
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 1375.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)