FAIRMol

Z57728545

Pose ID 4689 Compound 2821 Pose 626

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 Z57728545
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
65.9 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.60
Burial
96%
Hydrophobic fit
66%
Reason: strain 65.9 kcal/mol
strain ΔE 65.9 kcal/mol 1 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.637 kcal/mol/HA) ✓ Good fit quality (FQ -13.96) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (65.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-34.383
kcal/mol
LE
-1.637
kcal/mol/HA
Fit Quality
-13.96
FQ (Leeson)
HAC
21
heavy atoms
MW
302
Da
LogP
-1.34
cLogP
Strain ΔE
65.9 kcal/mol
SASA buried
96%
Lipo contact
66% BSA apolar/total
SASA unbound
501 Ų
Apolar buried
315 Ų

Interaction summary

HB 14 HY 15 PI 1 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 rank1.187Score-34.383
Inter norm-1.747Intra norm0.110
Top1000noExcludedno
Contacts14H-bonds14
Artifact reasongeometry warning; 7 clashes; 1 protein clash; 7 cofactor-context clashes; high strain Δ 65.9
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 NAP301 PHE97 PRO210 SER207 TRP221 TYR174 VAL206

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 overlap14Native recall0.74
Jaccard0.74RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
626 1.187320291425969 -1.74729 -34.383 14 14 14 0.74 0.60 - no Current
637 2.774211074879225 -1.33631 -29.5873 12 14 0 0.00 0.00 - no Open
638 3.735364597790352 -1.09287 -26.3826 8 15 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 -34.383kcal/mol
Ligand efficiency (LE) -1.6373kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.965
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 302.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.34
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 65.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 174.85kcal/mol
Minimised FF energy 108.96kcal/mol

SASA & burial

✓ computed
SASA (unbound) 501.3Ų
Total solvent-accessible surface area of free ligand
BSA total 480.2Ų
Buried surface area upon binding
BSA apolar 314.8Ų
Hydrophobic contacts buried
BSA polar 165.4Ų
Polar contacts buried
Fraction buried 95.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1463.7Ų
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 919.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)