FAIRMol

Z19651549

Pose ID 13437 Compound 1570 Pose 558

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 Z19651549
PDB9IFH↗

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 strong SASA done
Strain ΔE
10.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
45%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.768 kcal/mol/HA) ✓ Good fit quality (FQ -6.55) ✓ Strong H-bond network (6 bonds) ✓ Good burial (45% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Moderate strain (10.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-16.119
kcal/mol
LE
-0.768
kcal/mol/HA
Fit Quality
-6.55
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
3.21
cLogP
Strain ΔE
10.7 kcal/mol
SASA buried
45%
Lipo contact
66% BSA apolar/total
SASA unbound
525 Ų
Apolar buried
156 Ų

Interaction summary

HB 6 HY 7 PI 1 CLASH 1

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.851Score-16.119
Inter norm-0.896Intra norm0.128
Top1000noExcludedno
Contacts7H-bonds6
Artifact reasongeometry warning; 7 clashes; 1 protein clash
Residues
ASN402 GLU467 LYS407 PHE396 SER394 SER395 THR397

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 overlap5Native recall0.62
Jaccard0.50RMSD-
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
551 -0.10966209886901078 -1.29964 -25.3355 2 13 0 0.00 0.00 - no Open
532 1.0046581056658084 -1.50673 -28.6964 8 13 0 0.00 0.00 - no Open
558 1.8507984583927155 -0.895968 -16.1192 6 7 5 0.62 0.00 - no Current
548 2.3499413020302247 -1.40164 -21.5647 7 21 0 0.00 0.00 - no Open
536 2.4750002428206046 -1.35939 -27.4286 11 16 0 0.00 0.00 - no Open
542 2.63527126834114 -1.20429 -22.2029 6 11 0 0.00 0.00 - no Open
545 2.800134034659489 -1.54392 -31.1493 11 17 0 0.00 0.00 - no Open
541 3.544151329633376 -1.50159 -24.6005 12 18 0 0.00 0.00 - no Open
539 4.324614488326156 -1.4057 -25.737 10 16 0 0.00 0.00 - no Open
565 4.84275437333706 -1.34595 -23.6881 11 16 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 -16.119kcal/mol
Ligand efficiency (LE) -0.7676kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.547
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 301.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 39.17kcal/mol
Minimised FF energy 28.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 525.2Ų
Total solvent-accessible surface area of free ligand
BSA total 237.7Ų
Buried surface area upon binding
BSA apolar 156.4Ų
Hydrophobic contacts buried
BSA polar 81.2Ų
Polar contacts buried
Fraction buried 45.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2887.5Ų
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 1533.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)