FAIRMol

Z56768366

Pose ID 10715 Compound 194 Pose 550

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand Z56768366
PDB6RB5↗

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 medium Native mixed SASA done
Strain ΔE
18.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.50, Jaccard 0.35
Burial
58%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 45% of hydrophobic surface appears solvent-exposed (10/22 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 (-0.786 kcal/mol/HA) ✓ Good fit quality (FQ -7.51) ✓ Strong H-bond network (6 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (18.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-22.809
kcal/mol
LE
-0.786
kcal/mol/HA
Fit Quality
-7.51
FQ (Leeson)
HAC
29
heavy atoms
MW
426
Da
LogP
5.37
cLogP
Strain ΔE
18.7 kcal/mol
SASA buried
58%
Lipo contact
72% BSA apolar/total
SASA unbound
659 Ų
Apolar buried
273 Ų

Interaction summary

HB 6 HY 11 PI 0 CLASH 3 ⚠ Exposure 45%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (10/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22 Buried (contacted) 12 Exposed 10 LogP 5.37 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
Final rank4.159Score-22.809
Inter norm-0.833Intra norm0.047
Top1000noExcludedno
Contacts11H-bonds6
Artifact reasongeometry warning; 14 clashes; 2 protein clashes
Residues
ALA209 ALA90 ASN208 GLY214 GLY215 LYS211 LYS89 MET70 PRO212 PRO213 VAL88

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap6Native recall0.50
Jaccard0.35RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT16Atoms7551
Residues493Chains1
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:276; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
487 1.088329866091016 -1.17165 -32.6657 5 19 0 0.00 - - no Open
511 1.2374971441566485 -1.20348 -26.4937 4 18 0 0.00 - - no Open
548 1.4904529892984921 -0.920653 -22.5653 9 17 0 0.00 - - no Open
521 1.81825799653337 -0.897538 -26.5745 4 17 0 0.00 - - no Open
565 2.2544588790717133 -0.826268 -25.3055 8 11 0 0.00 - - no Open
530 2.3192700841994296 -0.96341 -25.2468 1 20 0 0.00 - - no Open
512 2.4932728018700403 -1.10026 -30.6157 5 16 0 0.00 - - no Open
541 2.508845732894417 -0.876449 -24.5843 1 18 0 0.00 - - no Open
522 2.531497306555514 -0.838818 -22.236 1 15 0 0.00 - - no Open
543 2.556193085876479 -0.766219 -16.5141 5 18 0 0.00 - - no Open
503 2.6989153506438197 -0.909917 -24.0506 6 16 0 0.00 - - no Open
508 3.0900948345735757 -0.897584 -21.3907 7 15 0 0.00 - - no Open
516 3.307089045836197 -0.707354 -18.8371 3 12 0 0.00 - - no Open
499 3.642356120158013 -1.12423 -30.5543 8 18 0 0.00 - - no Open
511 3.6596004503079134 -0.851044 -25.8511 6 13 0 0.00 - - no Open
504 4.110164392350293 -1.09071 -27.3774 9 16 0 0.00 - - no Open
550 4.159361593789174 -0.833109 -22.8091 6 11 6 0.50 - - 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 -22.809kcal/mol
Ligand efficiency (LE) -0.7865kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.508
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 425.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.37
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 74.95kcal/mol
Minimised FF energy 56.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 659.1Ų
Total solvent-accessible surface area of free ligand
BSA total 380.9Ų
Buried surface area upon binding
BSA apolar 272.9Ų
Hydrophobic contacts buried
BSA polar 108.0Ų
Polar contacts buried
Fraction buried 57.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3073.1Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1547.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)