FAIRMol

OHD_TB2021_62

Pose ID 10906 Compound 897 Pose 63

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand OHD_TB2021_62
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
21.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.39, H-bond role recall 1.00
Burial
73%
Hydrophobic fit
92%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.639 kcal/mol/HA) ✓ Good fit quality (FQ -6.44) ✓ Good H-bonds (4 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ High strain energy (21.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-22.355
kcal/mol
LE
-0.639
kcal/mol/HA
Fit Quality
-6.44
FQ (Leeson)
HAC
35
heavy atoms
MW
487
Da
LogP
2.42
cLogP
Final rank
2.7437
rank score
Inter norm
-0.636
normalised
Contacts
20
H-bonds 7
Strain ΔE
21.6 kcal/mol
SASA buried
73%
Lipo contact
92% BSA apolar/total
SASA unbound
837 Ų
Apolar buried
562 Ų

Interaction summary

HBD 3 HBA 1 HY 7 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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
Jaccard0.39RMSD-
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
61 2.147324469089883 -0.752236 -20.2287 6 21 0 0.00 0.00 - no Open
63 2.743724114752983 -0.635951 -22.3547 7 20 9 0.75 1.00 - 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 -22.355kcal/mol
Ligand efficiency (LE) -0.6387kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.442
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 486.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.42
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.64kcal/mol
Minimised FF energy 38.08kcal/mol

SASA & burial

✓ computed
SASA (unbound) 837.3Ų
Total solvent-accessible surface area of free ligand
BSA total 607.6Ų
Buried surface area upon binding
BSA apolar 561.8Ų
Hydrophobic contacts buried
BSA polar 45.9Ų
Polar contacts buried
Fraction buried 72.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6685.5Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2150.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)