Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
19.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.58, Jaccard 0.46, H-bond role recall 0.40
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.354 kcal/mol/HA)
✓ Good fit quality (FQ -11.75)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (19.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-29.782
kcal/mol
LE
-1.354
kcal/mol/HA
Fit Quality
-11.75
FQ (Leeson)
HAC
22
heavy atoms
MW
297
Da
LogP
2.30
cLogP
Interaction summary
HB 7
HY 21
PI 4
CLASH 5
Interaction summary
HB 7
HY 21
PI 4
CLASH 5
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 rank | 1.865 | Score | -29.782 |
|---|---|---|---|
| Inter norm | -1.477 | Intra norm | 0.123 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
GLN166
GLY205
LEU208
MET163
NAP301
PHE171
PHE97
PRO167
SER95
TYR174
VAL164
VAL206
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| Residue summary | LEU: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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 220 | 0.3651391185133525 | -1.45139 | -23.7405 | 8 | 14 | 11 | 0.58 | 0.40 | - | no | Open |
| 192 | 0.4571207130802301 | -1.18119 | -19.2496 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 237 | 1.5063260990891212 | -1.13516 | -23.1709 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 1.5181578036895516 | -1.089 | -19.0581 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 243 | 1.7178078774494703 | -1.28667 | -20.7882 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 232 | 1.8651070569406785 | -1.47707 | -29.7815 | 7 | 16 | 11 | 0.58 | 0.40 | - | no | Current |
| 198 | 2.1445626433417684 | -1.42852 | -28.7517 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 2.3624501248232654 | -1.20095 | -22.4306 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 155 | 2.5177967963534 | -1.60533 | -28.0634 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 2.61548570124989 | -0.940053 | -20.2644 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 2.843997714984992 | -1.28647 | -22.6883 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 153 | 3.038012358487256 | -1.13257 | -24.4214 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 223 | 4.2149665993990615 | -1.33738 | -26.7053 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.782kcal/mol
Ligand efficiency (LE)
-1.3537kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.753
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
297.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.30
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.69kcal/mol
Minimised FF energy
29.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
529.9Ų
Total solvent-accessible surface area of free ligand
BSA total
520.8Ų
Buried surface area upon binding
BSA apolar
398.8Ų
Hydrophobic contacts buried
BSA polar
122.0Ų
Polar contacts buried
Fraction buried
98.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1536.1Ų
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
922.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)