FAIRMol

Z27152867

Pose ID 5205 Compound 3051 Pose 464

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
T08
T. brucei PTR1 T. brucei
Ligand Z27152867
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
33.1 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.40
Burial
85%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.816 kcal/mol/HA) ✓ Good fit quality (FQ -7.95) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (33.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (11)
Score
-25.290
kcal/mol
LE
-0.816
kcal/mol/HA
Fit Quality
-7.95
FQ (Leeson)
HAC
31
heavy atoms
MW
436
Da
LogP
2.82
cLogP
Strain ΔE
33.1 kcal/mol
SASA buried
85%
Lipo contact
79% BSA apolar/total
SASA unbound
710 Ų
Apolar buried
477 Ų

Interaction summary

HB 10 HY 24 PI 4 CLASH 4
Final rank1.104Score-25.290
Inter norm-1.027Intra norm0.186
Top1000noExcludedno
Contacts14H-bonds10
Artifact reasongeometry warning; 11 clashes; 5 protein contact clashes; 4 cofactor-context clashes; high strain Δ 33.1
Residues
ARG14 CYS168 LEU209 LYS13 MET213 NAP301 PHE171 PHE97 PRO210 SER207 TRP221 TYR174 VAL206 VAL211

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
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

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 overlap12Native recall0.63
Jaccard0.57RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
464 1.1035884702550751 -1.0268 -25.2902 10 14 12 0.63 0.40 - no Current
475 3.5716124818696806 -0.671523 -19.4736 7 9 0 0.00 0.00 - no Open
450 4.251747176641782 -0.874141 -27.3218 12 18 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 -25.290kcal/mol
Ligand efficiency (LE) -0.8158kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.948
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 436.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.82
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 92.80kcal/mol
Minimised FF energy 59.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 710.4Ų
Total solvent-accessible surface area of free ligand
BSA total 602.4Ų
Buried surface area upon binding
BSA apolar 477.2Ų
Hydrophobic contacts buried
BSA polar 125.2Ų
Polar contacts buried
Fraction buried 84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1700.2Ų
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 923.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)