FAIRMol

Z18551701

Pose ID 4733 Compound 345 Pose 670

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
T07
T. brucei PTR1 T. brucei
Ligand Z18551701
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
39.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.58, H-bond role recall 0.00
Burial
86%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.745 kcal/mol/HA) ✓ Good fit quality (FQ -7.26) ✓ Good H-bonds (3 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (39.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-23.107
kcal/mol
LE
-0.745
kcal/mol/HA
Fit Quality
-7.26
FQ (Leeson)
HAC
31
heavy atoms
MW
498
Da
LogP
4.09
cLogP
Final rank
1.9656
rank score
Inter norm
-0.998
normalised
Contacts
19
H-bonds 5
Strain ΔE
39.5 kcal/mol
SASA buried
86%
Lipo contact
74% BSA apolar/total
SASA unbound
720 Ų
Apolar buried
462 Ų

Interaction summary

HBA 3 HY 6 PI 4 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
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 overlap14Native recall0.74
Jaccard0.58RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

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
660 0.5295804964357603 -0.996473 -27.6652 2 20 0 0.00 0.00 - no Open
650 1.0837521999406954 -0.860182 -25.7656 1 18 0 0.00 0.00 - no Open
647 1.1057279554427575 -0.82458 -22.7668 3 18 0 0.00 0.00 - no Open
670 1.9655946151535648 -0.997941 -23.1066 5 19 14 0.74 0.00 - no Current
641 2.067400124768355 -0.847561 -27.4139 1 19 0 0.00 0.00 - no Open
665 2.3541405331674663 -0.636352 -16.7251 6 13 0 0.00 0.00 - no Open
659 2.467759077605822 -0.750771 -19.8725 6 12 0 0.00 0.00 - no Open
671 3.368417260105743 -0.961077 -24.6186 9 19 0 0.00 0.00 - no Open
659 5.142259304440157 -0.87636 -24.9893 10 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 -23.107kcal/mol
Ligand efficiency (LE) -0.7454kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.262
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 498.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.09
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 33.01kcal/mol
Minimised FF energy -6.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 719.6Ų
Total solvent-accessible surface area of free ligand
BSA total 622.0Ų
Buried surface area upon binding
BSA apolar 461.5Ų
Hydrophobic contacts buried
BSA polar 160.5Ų
Polar contacts buried
Fraction buried 86.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1679.3Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 904.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)