FAIRMol

Z56853873

Pose ID 11474 Compound 909 Pose 631

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 Z56853873
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
19.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.23, H-bond role recall 0.00
Burial
79%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes 37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.780 kcal/mol/HA) ✓ Good fit quality (FQ -7.36) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (19.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-21.838
kcal/mol
LE
-0.780
kcal/mol/HA
Fit Quality
-7.36
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
2.68
cLogP
Final rank
2.6135
rank score
Inter norm
-0.809
normalised
Contacts
15
H-bonds 2
Strain ΔE
19.4 kcal/mol
SASA buried
79%
Lipo contact
74% BSA apolar/total
SASA unbound
648 Ų
Apolar buried
381 Ų

Interaction summary

HBD 1 HBA 1 HY 6 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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 overlap5Native recall0.42
Jaccard0.23RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
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
621 1.4345497717291078 -1.0318 -28.9875 10 16 0 0.00 0.00 - no Open
624 1.9005361944032626 -0.963332 -23.5994 3 15 0 0.00 0.00 - no Open
633 2.034066149755648 -0.997448 -27.4985 5 16 0 0.00 0.00 - no Open
614 2.1205691892069596 -1.06766 -31.8052 5 10 0 0.00 0.00 - no Open
617 2.21543994317517 -0.943733 -25.4581 5 15 0 0.00 0.00 - no Open
636 2.2733624275643116 -0.935816 -24.4034 7 14 0 0.00 0.00 - no Open
631 2.613527185358712 -0.808865 -21.8381 2 15 5 0.42 0.00 - 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 -21.838kcal/mol
Ligand efficiency (LE) -0.7799kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.363
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.68
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 23.24kcal/mol
Minimised FF energy 3.86kcal/mol

SASA & burial

✓ computed
SASA (unbound) 647.6Ų
Total solvent-accessible surface area of free ligand
BSA total 512.8Ų
Buried surface area upon binding
BSA apolar 380.8Ų
Hydrophobic contacts buried
BSA polar 131.9Ų
Polar contacts buried
Fraction buried 79.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6446.1Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2082.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)