FAIRMol

OHD_TB2021_32

Pose ID 8160 Compound 990 Pose 30

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 OHD_TB2021_32
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
39.8 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.71
Burial
76%
Hydrophobic fit
64%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes 45% of hydrophobic surface appears solvent-exposed (5/11 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.266 kcal/mol/HA) ✓ Good fit quality (FQ -10.80) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Very high strain energy (39.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-26.588
kcal/mol
LE
-1.266
kcal/mol/HA
Fit Quality
-10.80
FQ (Leeson)
HAC
21
heavy atoms
MW
315
Da
LogP
0.76
cLogP
Final rank
4.1034
rank score
Inter norm
-1.421
normalised
Contacts
18
H-bonds 14
Strain ΔE
39.8 kcal/mol
SASA buried
76%
Lipo contact
64% BSA apolar/total
SASA unbound
523 Ų
Apolar buried
254 Ų

Interaction summary

HBD 1 HBA 10 HY 1 PI 1 CLASH 7

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

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
Jaccard0.68RMSD-
HB strict7Strict recall0.78
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
53 2.0678219040784587 -1.1129 -18.6613 2 18 0 0.00 0.00 - no Open
27 2.5586706727142268 -1.53566 -28.6459 10 20 0 0.00 0.00 - no Open
60 3.138126296306823 -1.2108 -14.0103 12 15 0 0.00 0.00 - no Open
30 4.103352352734614 -1.42106 -26.5876 14 18 15 0.79 0.71 - 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 -26.588kcal/mol
Ligand efficiency (LE) -1.2661kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.799
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 315.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.76
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 16.22kcal/mol
Minimised FF energy -23.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 522.8Ų
Total solvent-accessible surface area of free ligand
BSA total 394.9Ų
Buried surface area upon binding
BSA apolar 254.2Ų
Hydrophobic contacts buried
BSA polar 140.7Ų
Polar contacts buried
Fraction buried 75.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2436.5Ų
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 1383.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)