FAIRMol

Z56071560

Pose ID 10119 Compound 535 Pose 633

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand Z56071560
PDB9IFF↗

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
48.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.85, Jaccard 0.55
Burial
70%
Hydrophobic fit
73%
Reason: strain 48.5 kcal/mol
strain ΔE 48.5 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 52% of hydrophobic surface appears solvent-exposed (13/25 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 (-0.598 kcal/mol/HA) ✓ Good fit quality (FQ -6.12) ✓ Good H-bonds (5 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Extreme strain energy (48.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-22.113
kcal/mol
LE
-0.598
kcal/mol/HA
Fit Quality
-6.12
FQ (Leeson)
HAC
37
heavy atoms
MW
564
Da
LogP
4.66
cLogP
Final rank
3.0754
rank score
Inter norm
-0.656
normalised
Contacts
18
H-bonds 7
Strain ΔE
48.5 kcal/mol
SASA buried
70%
Lipo contact
73% BSA apolar/total
SASA unbound
818 Ų
Apolar buried
416 Ų

Interaction summary

HBA 5 HY 6 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap11Native recall0.85
Jaccard0.55RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
617 1.2286859477856493 -0.645289 -22.1086 3 18 0 0.00 - - no Open
604 1.3266441361771943 -0.860678 -32.0683 3 18 0 0.00 - - no Open
607 1.6982015379180018 -0.786127 -23.3734 7 17 0 0.00 - - no Open
620 3.0402899482083474 -0.753862 -19.3978 4 12 0 0.00 - - no Open
614 3.0543374942600416 -0.713983 -28.0903 2 18 0 0.00 - - no Open
618 3.0637516082477028 -0.704842 -27.8068 2 17 0 0.00 - - no Open
633 3.075363984433379 -0.65572 -22.113 7 18 11 0.85 - - no Current
630 3.1325723545274675 -0.679026 -25.8742 9 21 0 0.00 - - no Open
616 4.10639197949174 -0.722302 -26.282 8 17 0 0.00 - - no Open
633 4.4909211152057775 -0.744179 -23.8511 8 18 0 0.00 - - no Open
631 5.0140432502219925 -0.734809 -23.4523 5 15 0 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 -22.113kcal/mol
Ligand efficiency (LE) -0.5976kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.119
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 564.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.66
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 48.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -36.97kcal/mol
Minimised FF energy -85.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 818.2Ų
Total solvent-accessible surface area of free ligand
BSA total 573.2Ų
Buried surface area upon binding
BSA apolar 416.4Ų
Hydrophobic contacts buried
BSA polar 156.8Ų
Polar contacts buried
Fraction buried 70.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3049.1Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1579.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)