FAIRMol

OHD_MAC_63

Pose ID 8478 Compound 4065 Pose 348

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 OHD_MAC_63
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
41.3 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.79, Jaccard 0.52, H-bond role recall 0.43
Burial
83%
Hydrophobic fit
84%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.709 kcal/mol/HA) ✓ Good fit quality (FQ -7.10) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (41.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-24.116
kcal/mol
LE
-0.709
kcal/mol/HA
Fit Quality
-7.10
FQ (Leeson)
HAC
34
heavy atoms
MW
471
Da
LogP
4.22
cLogP
Final rank
4.9786
rank score
Inter norm
-0.880
normalised
Contacts
25
H-bonds 11
Strain ΔE
41.3 kcal/mol
SASA buried
83%
Lipo contact
84% BSA apolar/total
SASA unbound
744 Ų
Apolar buried
517 Ų

Interaction summary

HBD 2 HBA 6 HY 3 PI 3 CLASH 7

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 overlap15Native recall0.79
Jaccard0.52RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue3HB residue recall0.43

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
348 4.978645910603506 -0.880116 -24.116 11 25 15 0.79 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 -24.116kcal/mol
Ligand efficiency (LE) -0.7093kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.097
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 471.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.22
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 124.05kcal/mol
Minimised FF energy 82.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 743.8Ų
Total solvent-accessible surface area of free ligand
BSA total 616.4Ų
Buried surface area upon binding
BSA apolar 517.0Ų
Hydrophobic contacts buried
BSA polar 99.4Ų
Polar contacts buried
Fraction buried 82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2650.5Ų
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 1427.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)