FAIRMol

Z44847963

Pose ID 4493 Compound 386 Pose 430

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
T07
T. brucei PTR1 T. brucei
Ligand Z44847963
PDB6RX6↗

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
31.3 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.80
Burial
80%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
2 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.129 kcal/mol/HA) ✓ Good fit quality (FQ -11.00) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (31.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (14)
Score
-35.013
kcal/mol
LE
-1.129
kcal/mol/HA
Fit Quality
-11.00
FQ (Leeson)
HAC
31
heavy atoms
MW
430
Da
LogP
5.28
cLogP
Strain ΔE
31.3 kcal/mol
SASA buried
80%
Lipo contact
75% BSA apolar/total
SASA unbound
727 Ų
Apolar buried
439 Ų

Interaction summary

HB 9 HY 24 PI 5 CLASH 4

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 rank1.123Score-35.013
Inter norm-1.099Intra norm-0.030
Top1000noExcludedno
Contacts16H-bonds9
Artifact reasongeometry warning; 14 clashes; 4 protein contact clashes; 4 cofactor-context clashes; high strain Δ 31.3
Residues
ALA96 ARG14 CYS168 LEU208 LEU209 LYS178 MET169 MET213 NAP301 PHE171 PHE97 PRO210 SER95 TRP221 TYR174 HIS267

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap13Native recall0.68
Jaccard0.59RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
430 1.123128311050852 -1.09943 -35.0127 9 16 13 0.68 0.80 - no Current
426 1.276767181328564 -1.03765 -27.4665 7 11 0 0.00 0.00 - no Open
461 1.476372703816213 -0.919152 -22.5547 4 18 0 0.00 0.00 - no Open
505 2.272725915955015 -0.896059 -31.1212 6 18 0 0.00 0.00 - no Open
412 2.595705842520432 -0.930582 -22.1691 7 11 0 0.00 0.00 - no Open
480 2.7191745516353594 -0.998852 -30.5149 7 16 0 0.00 0.00 - no Open
432 2.7494314954702257 -0.737507 -24.9974 1 17 0 0.00 0.00 - no Open
479 2.7843928705051484 -0.713014 -21.158 3 13 0 0.00 0.00 - no Open
500 2.791217765151704 -0.947142 -35.2818 6 18 0 0.00 0.00 - no Open
519 2.8617363901087467 -0.750125 -25.1003 6 14 0 0.00 0.00 - no Open
468 2.90635541192479 -0.798773 -25.6886 8 15 0 0.00 0.00 - no Open
441 2.9238440516247857 -0.997616 -30.3793 6 15 0 0.00 0.00 - no Open
468 3.20302513162988 -0.824135 -23.5686 7 9 0 0.00 0.00 - no Open
457 3.6279625865993608 -1.05901 -33.3892 7 17 15 0.79 0.60 - no Open
498 4.00190802340201 -0.862379 -25.6577 7 17 0 0.00 0.00 - no Open
458 5.080933656035169 -0.767574 -22.0757 6 18 0 0.00 0.00 - no Open
458 5.444083752190545 -1.06966 -30.8753 11 29 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 -35.013kcal/mol
Ligand efficiency (LE) -1.1294kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.003
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.28
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 133.01kcal/mol
Minimised FF energy 101.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 727.2Ų
Total solvent-accessible surface area of free ligand
BSA total 585.6Ų
Buried surface area upon binding
BSA apolar 439.1Ų
Hydrophobic contacts buried
BSA polar 146.5Ų
Polar contacts buried
Fraction buried 80.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1685.5Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 946.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)