FAIRMol

Z20127922

Pose ID 13548 Compound 3133 Pose 669

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z20127922
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 high Native strong SASA done
Strain ΔE
21.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 1.00
Burial
62%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.374
ADMET + ECO + DL
ADMETscore (GDS)
0.381
absorption · distr. · metab.
DLscore
0.416
drug-likeness
P(SAFE)
0.25
GDS classification
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.589 kcal/mol/HA) ✓ Good fit quality (FQ -5.99) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (21.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-21.211
kcal/mol
LE
-0.589
kcal/mol/HA
Fit Quality
-5.99
FQ (Leeson)
HAC
36
heavy atoms
MW
519
Da
LogP
4.37
cLogP
Final rank
2.9762
rank score
Inter norm
-0.540
normalised
Contacts
15
H-bonds 3
Strain ΔE
21.6 kcal/mol
SASA buried
62%
Lipo contact
74% BSA apolar/total
SASA unbound
790 Ų
Apolar buried
362 Ų

Interaction summary

HBD 1 HBA 1 HY 6 PI 2 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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.35RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
669 2.242959162236587 -0.630998 -24.4217 2 16 0 0.00 0.00 - no Open
658 2.348686823393062 -1.02818 -37.7301 4 16 0 0.00 0.00 - no Open
666 2.6812968608128886 -0.619624 -21.6677 4 24 0 0.00 0.00 - no Open
647 2.681307657453689 -0.654945 -24.3869 1 15 0 0.00 0.00 - no Open
669 2.976194309743088 -0.539639 -21.2114 3 15 6 0.75 1.00 - no Current
677 3.703549043285708 -0.923151 -32.1561 6 23 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 -21.211kcal/mol
Ligand efficiency (LE) -0.5892kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.989
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 518.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.37
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 31.61kcal/mol
Minimised FF energy 10.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 790.2Ų
Total solvent-accessible surface area of free ligand
BSA total 489.8Ų
Buried surface area upon binding
BSA apolar 362.2Ų
Hydrophobic contacts buried
BSA polar 127.7Ų
Polar contacts buried
Fraction buried 62.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3193.3Ų
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 1517.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)