FAIRMol

OHD_TbNat_104

Pose ID 10926 Compound 579 Pose 83

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand OHD_TbNat_104
PDB5S9T↗

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
53.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 1.00
Burial
75%
Hydrophobic fit
67%
Reason: strain 53.6 kcal/mol
strain ΔE 53.6 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Alert DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.670 kcal/mol/HA) ✓ Good fit quality (FQ -6.53) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Extreme strain energy (53.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-20.783
kcal/mol
LE
-0.670
kcal/mol/HA
Fit Quality
-6.53
FQ (Leeson)
HAC
31
heavy atoms
MW
436
Da
LogP
-0.56
cLogP
Final rank
4.0609
rank score
Inter norm
-0.820
normalised
Contacts
18
H-bonds 8
Strain ΔE
53.6 kcal/mol
SASA buried
75%
Lipo contact
67% BSA apolar/total
SASA unbound
682 Ų
Apolar buried
344 Ų

Interaction summary

HBD 3 HBA 3 HY 5 PI 2 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.43RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
84 1.0179927732673884 -1.02326 -25.6202 10 15 0 0.00 0.00 - no Open
87 3.2642859531252832 -0.996734 -27.8364 12 13 0 0.00 0.00 - no Open
86 3.3606023215307887 -0.929678 -30.7755 8 21 0 0.00 0.00 - no Open
94 3.411734690087445 -0.925891 -27.3176 9 21 0 0.00 0.00 - no Open
66 3.4554389482171013 -0.84221 -25.2275 7 15 0 0.00 0.00 - no Open
83 4.060877043540257 -0.820497 -20.7829 8 18 9 0.75 1.00 - no Current
81 4.253628773031853 -0.609689 -21.6506 7 10 0 0.00 0.00 - no Open
66 4.689246763870224 -0.774342 -20.4763 10 15 0 0.00 0.00 - no Open
45 5.218613317744509 -0.936281 -18.0731 14 18 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 -20.783kcal/mol
Ligand efficiency (LE) -0.6704kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.531
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 436.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.56
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 53.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 184.10kcal/mol
Minimised FF energy 130.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 681.8Ų
Total solvent-accessible surface area of free ligand
BSA total 510.4Ų
Buried surface area upon binding
BSA apolar 343.7Ų
Hydrophobic contacts buried
BSA polar 166.7Ų
Polar contacts buried
Fraction buried 74.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6485.2Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2062.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)