FAIRMol

Z49724748

Pose ID 13439 Compound 42 Pose 560

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z49724748
PDB9IFH↗

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 strong SASA done
Strain ΔE
30.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.00
Burial
48%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
1 protein-contact clashes 59% of hydrophobic surface appears solvent-exposed (10/17 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 (-0.782 kcal/mol/HA) ✓ Good fit quality (FQ -7.11) ✓ Good H-bonds (5 bonds) ✓ Good burial (48% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (30.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-19.557
kcal/mol
LE
-0.782
kcal/mol/HA
Fit Quality
-7.11
FQ (Leeson)
HAC
25
heavy atoms
MW
425
Da
LogP
3.43
cLogP
Final rank
3.1525
rank score
Inter norm
-0.864
normalised
Contacts
10
H-bonds 5
Strain ΔE
30.1 kcal/mol
SASA buried
48%
Lipo contact
76% BSA apolar/total
SASA unbound
595 Ų
Apolar buried
217 Ų

Interaction summary

HBD 3 HBA 2 HY 2 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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap7Native recall0.88
Jaccard0.64RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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: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
535 0.5554742205459879 -1.57398 -38.7698 15 16 0 0.00 0.00 - no Open
542 0.6301361565626356 -1.41362 -35.0467 13 20 0 0.00 0.00 - no Open
576 0.6491852433386276 -1.04323 -28.2743 6 16 0 0.00 0.00 - no Open
560 1.7385138815859185 -1.20275 -30.8924 10 14 0 0.00 0.00 - no Open
573 1.9408338434310477 -0.934882 -24.3666 8 14 0 0.00 0.00 - no Open
546 2.12496165439863 -1.12048 -28.9632 5 14 0 0.00 0.00 - no Open
573 2.1723358672917747 -0.917446 -22.622 4 14 0 0.00 0.00 - no Open
538 2.531466557515543 -1.11611 -27.7407 6 11 0 0.00 0.00 - no Open
551 3.031535954686285 -1.17336 -28.1011 5 18 0 0.00 0.00 - no Open
560 3.1524960599292062 -0.864105 -19.5566 5 10 7 0.88 0.00 - no Current
541 3.5786835219571276 -1.12988 -25.5305 10 18 0 0.00 0.00 - no Open
558 4.774003563882817 -1.42174 -34.3602 11 23 0 0.00 0.00 - no Open
567 5.672682983004134 -1.08344 -23.3257 13 17 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 -19.557kcal/mol
Ligand efficiency (LE) -0.7823kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.111
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 425.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.43
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 126.31kcal/mol
Minimised FF energy 96.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 594.9Ų
Total solvent-accessible surface area of free ligand
BSA total 285.4Ų
Buried surface area upon binding
BSA apolar 216.7Ų
Hydrophobic contacts buried
BSA polar 68.7Ų
Polar contacts buried
Fraction buried 48.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2974.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1530.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)