FAIRMol

Z49628846

Pose ID 8661 Compound 4037 Pose 531

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 Z49628846
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
11.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.57
Burial
76%
Hydrophobic fit
82%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.135 kcal/mol/HA) ✓ Good fit quality (FQ -10.46) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (11.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-29.508
kcal/mol
LE
-1.135
kcal/mol/HA
Fit Quality
-10.46
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
4.45
cLogP
Final rank
3.9253
rank score
Inter norm
-1.111
normalised
Contacts
16
H-bonds 11
Strain ΔE
11.0 kcal/mol
SASA buried
76%
Lipo contact
82% BSA apolar/total
SASA unbound
613 Ų
Apolar buried
382 Ų

Interaction summary

HBA 7 HY 2 PI 2 CLASH 6

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 overlap14Native recall0.74
Jaccard0.67RMSD-
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
544 1.1779734304124212 -0.717772 -18.7802 4 13 0 0.00 0.00 - no Open
561 1.5479325319184944 -0.791977 -18.7589 5 18 0 0.00 0.00 - no Open
531 3.9252532185645412 -1.11124 -29.5082 11 16 14 0.74 0.57 - no Current
566 3.9816480132556946 -0.955608 -19.9921 6 10 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 -29.508kcal/mol
Ligand efficiency (LE) -1.1349kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.456
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.45
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 109.62kcal/mol
Minimised FF energy 98.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 612.8Ų
Total solvent-accessible surface area of free ligand
BSA total 468.4Ų
Buried surface area upon binding
BSA apolar 382.0Ų
Hydrophobic contacts buried
BSA polar 86.4Ų
Polar contacts buried
Fraction buried 76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2595.1Ų
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 1390.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)